I think this all boils down to personal preference...Years ago when the market only had "tube glue" you used to get a horrid mess when gluing parts where the mating surfaces were painted...not to mention the mess it could make of your kit if you used to much glue.
I now have Ambroid Proweld, CA ( in various forumlas ), and have just the other day picked up Tamiya Thin Cement ( comes in a clear glass bottle with small built in brush ) though I have yet to use it as I'm restocking my diminished supplies ( since returning to the hobby ) before jumping into a kit.
A kit I had done about 3 years ago ( my one and only kit in ohh about 10 years ) I did things a little differently than how I was "taught" to do them.
I placed the parts in a sink with some Dawn and let them soak for a few minutes before rinsing and letting them dry overnight. After the parts dried over night I then "primed" everything using FLOQUIL model RR "white" primer from a spray can ( All the parts on this kit were molded in a "light gray", while not as bad as red or some other colors parts used to come molded in. ). Now in the past I had never really bothered to take these steps, I believe it helped as things went a little smoother than I ever remember them going.
I then "pre-painted" all of the parts while still on the sprue trees before doing any sub-assembly or further construction. ( This I have always done, but I may try something different with my next kit. )
Which method is best? Which ever one is best for you and gets you the results that you desire. I know one of the fellas that worked at the hobby shop recommended I "wash and prime" all my parts before final painting, as it would give the "color-coats" something to adhere too..So I tried it and will never go back.