Just as an example, this is what needs to be in the target field if you want to run it with the mediavps:
F:\Space\FreeSpace\fred2_open_3_6_10.exe -mod mediavps
(The path to the executable needs to be adjusted for your setup, obviously)
What your final command line will have to look like, I'll leave as an exercise for the reader.
Note that neither FRED nor FS2_Open read mod.inis; those are only used by the Launcher.
This means that in that Target field, you need to specify each mod you want to use in the right order.
That is, the command line should look like this:
fred2_open_3_6_10.exe -mod a,b,c
Where mod a will override data found in b, which in turn overrides data found in c.
Finally, table files (.tbl and .tbm) need to go in <mod>\data\tables.
For further education, I would like to recommend the FSWiki's
Modding portal.