Yeah, for most container plants you should isolate if you want to keep them healthy. They might be fine growing together, but keep in mind the roots will be competing for space and there will be a lot of root tangle going on, if one plant dies, you'll likely lose both. Because of this tangling, I don't think you can seperate easily after even a few months of growth.
As far as fertilization, all container plants will need regular fertilization. There are some nice organic fertilizers out there available. I'm using a slow release Osmocote (Not organic, but I think they make an O. version) for mine, you only need to fertilize every 4 months and it seems to be working well. (It is a 19-6-12.) If your plants aren't very green you would want more Nitrogen (I've used Dried Blood as an organic Nitrogen additive in my garden at home, you can get it at good garden stores.), if you want to encourage root growth or flowering you'll need more Phosphorus.
As far as pot size, you want to gradually scale up for the best results, basically, you want a pot that is as deep as your tree is tall. The plants do fine if the pot is not so big, but if you give them too much sun and the pot is not big enough, they'll get gangly and out of proportion and you risk needing to water all the time. If you go too big, the soil is going take too long to dry and you can run into mold and root rot.
My Chicago Micro-Lot is coming along, I'll be moving some plants outdoors for the summer and hope to install a self watering system this winter for some Yellow Bourbon and Pacamara that I'm starting....