When you download a mod, the mod's author will have done all of the work for you. The proper directory structure is already there; all that you need to do is copy and paste.
A different way of stating the same idea...
Say that you download a mod: TM-mod-awesome-weapon.zip
When you unzip TM-mod-awesome-weapon.zip, all that you should see is a folder called AddOns. The mod author will have created the proper directory structure, and placed the necessary files in all of the correct folders. All that you need to do is copy the AddOns folder into your root TreadMarks directory, and you are done. TreadMarks will now see and use any and all mods that you have placed into the AddOns folder.
as always, let us know how it goes, or if there are more questions.
one cautionary note here, which I have done before...
just be careful not to have a 2nd AddOns folder inside of the primary AddOns folder ...
any mods inside of the 2nd AddOns folder, accidentally inside of the primary AddOns folder, will be ignored by the game. There can be only one AddOns folder, found in the root TM directory.