I own several guitars, and typically run all of um with different tunings.

My cheapest guitar, I have dedicated as my low tuning guitar (for playing the drop C and B stuff). I first learned on here about going up on string size for lower stuff. So I bought some Ernie Ball "Not So Slinky" strings. These seemed to do the trick.....but.....the guitar just doesn't sound right. According to my tuner, its always in tune, but it just sounds terrible.

Are there any special steps to take when setting up a guitar to play lower tunings? I'm still pretty new to the technical side of guitars and I'm trying to learn how this stuff works.
intonation, maybe?
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Definitely sounds like an intonation problem. Relatively easy to fix, provided you have a decent tuner and the tools required.
...and intonation = "string length" = how well the guitar rings in tune when you move up (or down, i mean to frets 1->24) the fretboard

- As the (first) full octave is "filled" at 12th freth, you ought to check how well each string is in tune when fretted on the 12th. Then you act accordingly - depending on whether it's sharp or flat and your bridge type

- Tons of guides online.