Well I'm a new mod user and I have recently downloaded and successfully installed a few mods to wet my appetite, now I wanna get some more and play around.
But the problem I'm having is when a mod tells me to put a mesh and texture (and or sound) folder in the Oblivion data folder, that's fine, but what about my next mod? You can't have duplicate folders with the same name, so what am I supposed to do? Run one mod at a time?
This more than likely sounds like a very stupid question for those of you who have been doing this for years but this is my first day literally at using mods.

I'll restate my problem in case I worded it poorly:
What am I supposed to do when a mod tells me to put a mesh/texture/sound folder in the Oblivion data folder where all the ESPs go when I already have a mesh/texture/sound folder. It tells me it will replace them, which obviously isn't good, because they are duplicate names.
Thanks in advance for your patients and understanding.

They just merge together so there is no need to worry

Don't worry, you can just go ahead. Just overwrite it, there will be just one meshes folder. And unless it's specifically mentioned that a mod replaces something from another mod, nothing will be overwritten inside the meshes folder. Sometimes it's needed for updates or fixes of a mod, but that's when it's needed.

There will be, usually rare, where one mod will overwrite specific files. This is where order of installation becomes important (don't confuse this with load order). Read the docs provided with each mod and you will be fine. An example would be the Unofficial Oblivion Patch and a body-replacer. Both will have eg. armour meshes. UOP is installed first (fixes for vanilla) and the body-replacer second (meshes specific to that body), overwriting as necessary. Hope this isn't too confusing for you.

What the other says, but do yourself a big, big favour and learn to use OBMM or BAIN to install those mods. OBMM is the simplest to start with so I recommend that one.

OBMM or BAIN will remember which meshes, textures and other resources that were installed by which mod, so if you uninstall a mod, its resources gets uninstalled as well. There are many other advantages to using those, but this is a good enough reson in itself.

ai, although it'd be nice if more mods were omod ready....too many of them require manual installation and even if you make them into omods it wouldn't work because there is no omod installation script, so activating them could cause problems...when it comes to modding...there is a lot to read, and if you are willing, then stop installing and read about BAIN installation, i definitely need to read that thats for sure

The vast majority of mods can be made into an OMOD and installed without a problem. Only mods that have multiple install options or have archive structures that OBMM won't work with require extra prep.

What mcc84 said. To make an omod from a downloaded mod, do the following (written from memory):
1. In OBMM, click on the "Create" button
2. In the omod creation window that pops up, click "Add archive" (not Add file or Add folder).
3. Navigate to and select the downloaded archive (should be a .zip, .rar or .7z file)
4. If the archive contained omod converstion data, answer yes to import those and go to step 7
5. Fill in mod name and version yourself.
6. If the mod came with alternate esp files (e.g. HouseMod.esp and HouseMod - cobl.esp), right click on the one you don't want, in the plugin list of the window, and select "remove from omod".
7. Click on "Create" and let OBMM create the omod for you.

8. Now you have your omod. Double-click to activate it.

The only mods this doesn't work for, are mods that has multiple alternate sub folders where only the content of some folders are to be installed, and have no omod conversion data - and that is a very small minority of the mods.