Alignment of the chuck is not any different then you would do with a 4J independent chuck, except you use the adjustment screws as opposed to the chuck key. You want to use a quality 5C collet that has minimal run out and use a precision ground rod or the shaft of a end mill. Snug down the mounting screws holding the chuck to the back plate but do not over tighten. Use a dial or test indicator 0.0005" or better and adjust the opposing set screws for minimal run out while rotating the chuck (put the gearbox in neutral and gently turn the chuck). you should be able to get the run out to a few ten thousandth, then tighten up the chuck to the back plate and recheck the run out. Chuck should repeat within around 0.0004" or better, although 5C collets tend to be not as uniform with regard to TIR compared to ER collets.
Once set, you should not need further adjustment of the chuck, i.e. you pretty much set it and leave it. I recheck my Set-Tru type chucks occasionally. As others mentioned, you should always mount your chucks in the same position, often put a witness mark on the chuck and spindle. I only have one pinion on my 5C and 3J PBA set-tru chuck, those with multiple pinions usually have a master that should be used for final tightening.
