I got really far in the game (to disc 4) without paying much attention to what was junctioned.... I also spent a lot of time running around getting lost though, so I'm guessing I had pretty good levels for my characters for most of that time. Cerberus was the first anything to give me any sort of trouble, but after a quick scan, I unmade him.....

I think my main strategy was using Mad Rush right as soon as I got it. It's not like you NEED to cast magic on the lesser enemies. I also GF the snot out of anything that seems boss-like. I think that was pretty much it. The only spells I REALLY used were meltdown and flare.