I start off with naming my maps, e.g. blahblah_a1.pk3 (then a2… all the way to beta). I only make pk3 files if I want to export and test the map on my server.
Also it is a good thing to save a working map every now and then, like, when you have a blahblah_a5 map that compiles and runs fine, save it as blahblah_a5_working.map and continue working on the old blahblah_a5, this has saved me a lot of trouble especially in the begining when I was doing many mistakes.
You should also start out from the begining with using lights and doing complete test compiles (that’s what my computer usually does at nights anyways) - it is not always easy to find out what causes compiling errors and its’ not like your computer are doing anything else while you sleep?
If you really wanna be technical about it you should alse copy your .map file out on someplace safe, you never know when your computers’ gonna fail.