The example guitar we are going to use will be the Fender Jaguar HH. At this moment, you should've probably mounted new strings, stretched them, adjusted the truss rod and string height, and set up the string tree on the guitar. Once the guitar is tuned to pitch, before adjusting the action, make sure that you have already done the sound check with the guitar.
Step 1: Pre-Intonation Setup Check
Before you adjust the intonation, there are a few important steps to take. First, make sure that the guitar's truss rod, string tree, and string height is adjusted as necessary.
Step 2: Disconnect guitar from amp if not done so.
If you want to have a perfect intonation on your guitar, you should first disconnect the guitar from the amp to use the raw string sound as the baseline for intonation. For those who wish to customize their pickup height, it's not a big matter, so skip this step if you want to.
Step 3: Raw-Sound Intonation
From here, the intonation is simple. Fine-tune the open note on a string, then fret the harmonic note on the 12th fret. (TIP: Use a tuner to fine-tune as necessary!) The two notes should show and sound that they are equally in tune. If they are not, adjust the intonation by first de-tuning the string slightly, then adjust the intonation by using a Philips screwdriver to turn the small screws shown on the front, or back, of the saddle part of the strings where the strings rest on. Go clockwise to go flat, and go counter-clockwise to go sharp. This is VERY IMPORTANT that you ALWAYS intonate by the small amount at a time! Every time you intonate it, fine-tune the open note, and then fret the harmonic note again. If they are still not intonating, keep going until you find the perfect spot for your guitar's intonation! Once a string is finally intonated, move onto the next string, and repeat the process for the same string.
Also, this is VERY IMPORTANT that when you fine tune the open note with a tuner, ALWAYS TUNE UPWARDS! If you go sharp on your open note, de-tune it flat, stretch the string, and tune the open note again! This helps keep the strings stretched, and you'll always be sure that the strings will be perfectly intonated!
Step 4: Pickup Height Adjustment
Once all your strings are intonated, it's time to intonate the guitar's pickup height. Turn the amplifier on, and use a tuner to match the pickup sound to the raw sound. You only need to do this with low-E and high-E strings. When adjusting the pickup height, rise the pickup to go flat, and lower the pickup to go sharp. Remember, you must do this adjustment for all pickups, but be aware that they might not have the same pickup height as you might've expected! Most pickups have a reason as to why they have a distance from the strings! If you are customizing your pickup heights, this is no big deal.
Step 5: Shred!
Once you adjusted the pickup height, you're done! Just put away your maintenance kit, and shred to your bones!