I've been wanting to get some knowledge about alternate tunings, especially on making two guitars with different tunings play in harmony, having bands like Sonic Youth or American Football as example, but I'm kinda lost on where to find reading and lessons. I usually play in Standard half-step down or Drop C#, so finding a corresponding tuning would be a great place to start. Sorry in advance if this isn't the right section to ask about it.
The harmony isn't going to change with the tuning ... the scale shapes and chord shapes may.

If you're looking for a tuning that means the same shapes can be played on both to create useful harmony that's potentially tricky.

What have you got in mind?
Take this tab for example, where both guitars are in different tunings: https://tabs.ultimate-guitar.com/a/american_football/stay_home_ver3_tab.htm

For now I'm just messing around, so I took a song where both guitars are in the same tuning (in this case Drop C#) but I changed my tuning to open C#m with a capo on the fourth fret and messing around with my melodies. It sounds cool since I figured out where to place the capo according to the notation, but I'm still just guessing things around. I wanted to find more info about blending different tunings in a song and what I should study to develop this skill for future writing.
Try listening to a country or bluegrass band. All string instruments for the most part (guitar, fiddle, banjo, mandolin, steel guitar, bass, and dobro), but with completely different tunings. But a C note is a C note and a 3rd is a 3rd and a G chord is a G chord, regardless of instrument.

The problem is that you are thinking too much about tuning. Two guitars in different tunings both play the exact same notes (within the overlapping area of their range). Same with any string instrument in any tuning. You have to think about the actual notes rather than the physical location on the fretboard. So if you're harmonizing a melody in thirds in C, then CDEFG and EFGAB are thirds apart regardless of tuning.

One thing that is very difficult with new tunings, specifically ones with different intervals than standard, and therefore not simply transposed, is that you have to relearn the fretboard, making familiar scales and and voicings harder to find since they aren't where they were in standard. How well do you actually know your way around open C#m?

If you aren't particularly comfortable with that tuning (ie can't easily find scales, intervals, voicings, etc), it will be very difficult to harmonize since you don't know where anything is.
There's no such thing; there never was. Where I am going you cannot follow me now.
You're right, I'm thinking too much about tunings haha but it's because I'm a little intrigued by this combination thing, and that's exactly why I'm asking. And yes, I'm struggling with how a different tuning affects the fretboard but at the same time having a good time with the new discoveries and new sounds I'm finding on it. Still, your reply really cleared my vision a little. Any bluegrass/country recommendations? I've been curious about some blues too.
In the "About Me" section of my profile, I have a list of about 30 or 40 bluegrass and similar artists to check out representing the different eras from the earliest to modern.

Country is a lot harder than bluegrass because it is a lot more diverse. You have a lot more differences between eras and regional styles and subgenres than in bluegrass. Another thing to note is that in country, solo artists, mainly singers, are the well known musicians, with "bands" like you have in rock or whatever being less common. So most of these suggestions will be great singers that happened to have a talent at picking backing musicians or that had generally good session musicians. Another tricky thing is that rock, punk, metal, etc tends to be more album oriented, while country is more single oriented, similar to pop music.

Hank Williams is the best there ever was though, so start with him. After that...

It really depends. You can start back at Western swing, with Bob Wills, Milton Brown, and Spade Cooley (his crazy personal life aside) being the best. From there, honky-tonk was the big thing. Besides Hank, check out Ernest Tubb, Floyd Tillman, Lefty Frizzell, Webb Pierce, Faron Young, and the early recordings of George Jones.

From there, the genre really splits a lot into different sounds. On the one hand you have the polished sounds of Nashville country. This is basically the roots of what is called pop country. Over the past 50 plus years, the Nashville sound has kind of morphed to include whatever was popular at the time, which goes from the string ensemble-laden and reverb-drenched sounds of 60s pop, Yamaha DX-7 electric piano ballads of the 80s, and modern stuff that sounds like synth pop and post grunge. This was where all the real commercial success was, and not surprisingly it's also where you find the greatest inconsistencies in quality, with a very high ratio of bad to good music.

Some of the good ones to check out are (obviously) Johnny Cash, (again) George Jones, Ray Price, Dolly Parton, Tammy Wynette, Alabama, The Oakridge Boys, Crystal Gayle, Loretta Lynn, and like a million others. All of them put out some very good singles and some very bad ones. Again, not much consistency here, but the good tunes like City Lights, Crazy Arms, and He Stopped Loving Her Today are genre defining classics so you can't really just skip over all of it. Anything from the last 20 years though can be skipped though since it's mostly awful, although a couple of Shania Twain songs and Casidee Pope are guilty pleasures.

In response to the slick sounds of Nashville, there were other rougher, more rootsy subgenres of in the 60s and 70s, particularly the Bakersfield sound, Outlaw country, and country-rock, and trucker country. Artists to check out in those styles include Buck Owens, Merle Haggard, Willie Nelson, David Allen Coe, Kris Kristofferson, Emmylou Harris, Hank Williams Jr, Waylon Jennings, Flying Burrito Brothers, New Riders of the Purple Sage, The Byrds (later material), Charlie Daniels, Adleep at the Wheel, and the great Red Sovine.

In the 80s and 90s, this continued with what is called neo-traditional country, which, while commercially very successful, resembled older styles like honky-tonk. A few to check out are Randy Travis, Alan Jackson, George Strait, Ricky Skaggs, and Junior Brown.

You also have stuff like psychobilly, cowpunk, and alt country. These are styles that evolved in the 70s/80s and incorporated punk, gothic rock, metal, and other types of music. This is a very diverse bag of artists and a little something for everyone. The Reverend Horton Heat is a personal favorite. Also one of the most well known alt country groups is a Canadian band called Luther Wright and The Wrongs, who are best known for doing an slt country recording of the entirety of Pink Floyd's album The Wall. And of course there is Hank III (yup, another Hank Williams).

Also you might be interested in guitarists. Some guys like Chet Atkins, Jimmy Bryant, Duane Eddy, Joe Maphis, and a bunch of other guys that were known probably more for instrumental guitar work. Other guitarists to check out are Danny Gatton, Johnny Hilland, Will Ray, James Burton, Ray Flacke, and Brent Mason. Mason in particular stands out because of the sheer volume of session work he has done, totalling like 1500 album credits over the past 30 years.
There's no such thing; there never was. Where I am going you cannot follow me now.
Make or find a table of what notes are in each major and minor chord to get started. Will give you the idea of what notes interact with each other to create harmonies.

This might help get you started http://www.essm.net.au/chords/
Visit my music school site for advice on gear, music theory and lessons.
Last edited by Rhys Lett ESSM at Jan 1, 2016,