For ships i tend to prime on the spur and touch up if needed. The primer will increase the dry time of the glue (i use model master: liquid cement), but it bonds just as good as if there was no paint. No problems with super glue.
As for priming everything else, I rarely prime on the spur tree. I assemble everything untill it is all ready to be painted, i then prime all sub sections and individual parts.
For small parts i use strips of painters green or blue tape turned upside down and itself taped at the ends to a piece of cardboard, this will keep them from moving. I use a spray can to prime (
Here is a link to a post that i made on my favorite primer), i spray outside due to fumes, i also took a cardboard box and cut away the the top and one side to make a wind break.
I never paint on the spur, but this is mostly a lack of forsight as some parts that i would paint by itself have the spur tree attached to a non visable area.
Mongol General: Conan, What is best in life?
Conan: To crush your enemies, see them driven befor you, and hear the lamentations of the woman!