Hi Commasplice, I use mod manager and can confirm that it works fine with all *.package and python *.zip files. It doesn't automatically recognise the newer *.ts4script format but can be made to work with it.
When you install mod manager it creates it's own mods folder on the c drive (in the install folder if that is on c), all the mods/cc are placed inside this mods folder. When you select the mods in Mod manager it copies those mods to the sims 4 mods folder. As long as you can find the mods folder created by mod manager you can copy any file you want into it and select/deselect that file from inside Manager to add or remove it from the game. Any ts4script file you add in this way will show with an error inside mod manager but work fine in game.
Also Mod Manager can only cope with 1 level of sub folder, so mods/hair is fine but mods/hair/child won't work.
A useful feature of Mod Manager is that you can click on the title of any sub folder to highlight all the files inside that folder so you can select/deselect them in one go. I use this a lot to remove mods that are not tournament legal but used for fun games.
Hope this helps, happy simming.