Now you need to adjust the saddles up higher so that the thicker strings will clear the frets, then you will probably need to release a little tension on the truss rod to move the headstock forward, this gives more clearance to the strings at the top of the neck. As far as innotation that is simple, get the sting in perfect pitch then (connected to a tuner) do a harmonic note on the 12th fret and if it is not also in perfect pitch you need to turn the screws on the bottom of the trem until it is, one way will make it sharp the other flat, the direction you turn them in depends on where the pitch is. Once you turn the screw retune the string and do the harmonic again and see where you're at, this is innotation. Now, to make this clear the innotation screws are the HORIZONTAL ones at the bottom of the trem, NOT the vertical ones between the trem and the pickup, those are the ones that WILL destroy the knife edge if you don't know what you are doing, leave those alone. There should be some good videos on youtube to demo all of the stuff you need to know, just look for ones where there are either a lot of good reviews or a lot of followers on the channel, generally the info in those is good. Setting up your own guitar is a great thing to be able to do because generally a tech will either not set it up like you want it, they will do it their way or it will just never feel "just right" but by making your own adjustments you can get it exactly where you want it.