You can only add a few mods in the manager at a time, as adding too many mods will cause the manager to remove those mods when reloading the game. This will make you have to reload the game multiple times to get the manager to add in all the mods you want. Very time consuming and annoying, especially if you're planning to play with 100+ mods. Saving the modlist doesnt help as it doesnt seem to recognize the extra mods you added.