I thought I'd give this mod manager a try. I like it so far but I have a couple of questions. What is this mod/priority order in the left pane? Load order is on the right I assume, and that's all I've had to worry about before. So how does this other list factor in? Also, since LOOT is basically integrated into this program, should I bother to install and use that separately?

Question #1 : The left pane is Install Order. This shows the order in which you have mods installed. This can be extremely useful for mods that conflict. For example lets say Mod A is a full armor overhaul mod that changes the look of several armors while keeping their vanilla names and file location and Mod B changes 1 of those Armors in a style that is different from A. Whichever is installed last wins. So if you install A then B, B's changes will win and vice versa. This is just a more sophisticated way of showing you what you will get in game.

If you click on a mod you see other mods highlight if they conflict, if you double click the mod a new window will appear and you can click the Conflicts tab and see what exactly is conflicting.

On a more advanced note if you have Mod A and B and have A installed first. If you want some changes from B to win, but not all of them (you want some of the changes from A to win over B ) you can go into B and select the files you dont want to win and select Hide. These will "Hide" the files and allow the conflicting files from A to "win".

Question #2 : No you do not need to install LOOT a second time.