I'm not sure I understand what you are asking. If the footage files are stored realtive to the project, you only need to re-create this structure, regardless of whether the project can be collected or not, i.e.
--- folder 1
--- folder 2
--- folder 3
AE never stores more path info than it has to, so you can keep projects portable. If your files are larger, you should manually copy them to such a structure and then use the respective replace footage commands to update the path info inside the project. Once done, you can manaulyl copy the files to the watch folder and it will render just as well.
My man. The replace footage step was what I was missing. Nice.
Thank you so much for your help, we are now rendering files larger then 2gb and without copying the files and duplicating them on our network drives. Could you also give us a hand with trying to optimize our render farm machines so that they will render as quickly as possible. We have two machines dedicated to rendering that have 4GB of ram and 2.53 ghz xeon processors that are showing 8 cpus in the task manager of the machines. When we are rendering only 4 of the CPUs show activity and we are unsure what setting in the preferences of our render engines below would be the absolute best for rendering speed, and to get those other 4 cpus to kick in. thank you in advance.
You don't necessarily want to use all 8 of your 8 CPUs for Render Multiple Frames Simultaneously multiprocessing. See this article for details:
See this article and the pages that it points to for additional performance and memory allocation tips:
Mr. Kopriva-Man® has already pointed you to all the right answers. On your systems, you will probably never be able to use more than two physical cores. 4GB is really not much and stocking up on RAM is highly recommended. I would, however, add, that there is no all out perfect render setting for MP. This can hugely vary with the kinds of features, effects and footages you use - HD footage with lots of effects is more memory and I/O intense than stuff you only created with AE text layers and particles. One favors RAM and fast disks, the other processing power. It realyl depends.