First, you do not need any supermods with MaGui to my (limited) knowledge. However, MaGui will work with supermods (read any readme files in the bundles you find). I would suggest you choose one of the supermods (LSH3, NYGM, GWX or WAC4). They add a lot to the game.
Second, to install mods (except supermods which will have their own setup files), use JSGME, a standalone program to enable mods for a wide range of games.
Link to JSGME
http://www.subsim.com/radioroom/down...o=file&id=4725
Just read the instructions, install the program and via JSGME, install the mods of your choice.
NOTE: If you want a supermod AFTER having installed individual mods, UNINSTALL all the individual mods through JSGME BEFORE installing the supermod. The supermods should be installed on a clean, unmodded install of SH3, patched up to 1.4b.