I like to get the neck as flat as possible with the bass tuned up then just let a smidge of relief in so if you hold down the 1st fret and 13th fret you can just about get the string to ring out when tapped in the middle (thumb on 13th and 1st finger to tap), once that is set you cant do anything else and most ebmm basses already have a shim in the neck pocket, adjust the saddles to what you want, I use an allen key (2mm I think) under the 12th fret wire and the back of each string across the board, tune and intonate until it rings like a bell
My 2010 SR5 has a slightly high fret that needs a tiny dressing if anyone wanted it super low but its fine for me and if it rsttles I know its time to adjust the truss for the seasonal change, I see people suggesting people altering the saddle heights to restore basses back to normal but once you have it nailed all you EVER need to do is turn the wheel of fortune to make it play and intonate perfectly, brilliant.