Honestly, I don't think there is a way to separate fry out that isn't space consuming...unless you have a very small spawn.

Even barracks take up quite a bit of room, though are probably the most organized way of going about it....
A large plastic storage bin with a heater, as you mentioned, where you can float the cups would work just fine, though I'm not sure how that would be more space-efficient....you'd need one big enough to be able to hold all of your jars, so it'd take up just the same amount of space as just setting the jars next to one another I'd imagine....
Though the bin with a heater is definitely a good idea if you can't keep your room temp warm and stable. ;)
No matter what though, you'll need a LOT of space if you plan on a spawn larger then 20 or 30....I think thats just one of the downsides of breeding