Does anyone know how to run multiple mods at the same time? Also how would i edit the civ4config file to have them start automatically. i've only been successfull at having one auto start when the game loads.

Manual editing, lots of it.

I've tried and combined some.

It's hard, especially when multiple files overlap.

My suggestion is that use Win32 diff and pactch from GNU.

Make diff files of each MOD files and original unmodified game file.
Then, merge the diff files with text merge utility like windmerge.
Copy selected (affected) files to CustomAsserts folder.
Apply the merged diff file to them.

If the changes in two mods are overlapping, it needs manual merging.

I think that the every MODS creator should distributed their mod file as patch file.
Someone (Firaxis) should make some utility to automate this process.

Or the mod shuld be distributed as INSTALL.MSI file that automates installation.