For upgrading equipment, fuse two lower level equips together before adding it to what you want to upgrade. It gives more exp, saves gold, and helps preserve space. I haven't had any inventory issues doing it this way and I usually only upgrade +10 equips. If you want a cheap stats boost early on in the game, its probably fine to upgrade some +9 rings, but the other stuff is common enough that I feel like its a waste to upgrade anything but +10 (or in the case of earrings, a waste in general unless you have nothing better). Character accessories are a good equipment dump too if you have nothing better, they're just expensive and don't give huge bonuses.
When I don't have the space/gold I just don't pull new equips. I think I was sitting at 5k equip seeds for a while because I was saving gold to upgrade an event girl.