I have a question about SKSE. My understanding is this creates a new little icon that needs to be clicked in order to run skyrim, Currently I run skyrim through the NMM. Will my mods still load properly if I use the SKSE icon instead? Is there a way to point NMM to the SKSE start instead of the vanilla one?

There are a lot of neat mods that require SKSE but I want to make sure I understand how to start it up correctly before I install it. The SKSE tutorial does an excellent job guiding through the installation process but is pretty vague about what to do after that. Help would be great!

If you start Skyrim through NMM, NMM executes the TESV.exe. But you can also let it execute the skse_loader.exe:

http://imgur.com/sSagKHs

Does NMM close down automatically if starting the game via it? Otherwise I don't get why to do it as it will take up resources that you'd rather let the game have. Better to make a short cut to the SKSE loader, place it on the desktop - and start the game via it.

yes NMM close down when launching game via it though making a skse shortcut is more profitable

You can choose if you want it to close or not when you start skyrim.