I'm sure I read about it in the documentation, but I can't find it for some reason.

Reason being, I need to re-order them because for some reason the morrowind patch comes before bloodmoon in my load order, and I remember hearing somewhere that that is really bad. Am I right??

Lastly, can I re-order them without messing up my save game?

Highlight the one you wanna move, and then you'll see a date on the right. Change that date to move it. Like if you wanna move it above a certain mod, and that certain mod's date is 9/6/2008, you'll change the date on the one you're moving to 9/7/2008 or something higher.

There's a fantastic tool called "Mlox" that sorts most of the popular mods for you. It also gives handy notes on conflicts and such. You can find it http://code.google.com/p/mlox/wiki/Mlox.

Well, it's directly at the top of the documentation... not sure how you missed it.
http://wryemusings.com/Wrye%20Mash.html

Yes.
After making the changes, just Update/Re-Sync your save file. Repairing it is also a good idea.
Don't know how to do those things? No worries, the Mash doc has all the info.

Having the Code Patch installed can also alleviate some problems associated with altering mods mid-game. But keeping your save files updated with Mash is a good habit.

If you still have minor conflicts in your loadorder you can always read the readme, because some mods do have information about a correct loadorder and if the information is useful just report your findings to the http://www.gamesas.com/index.php?/topic/1167004-relz-mlox-a-tool-for-anolyzing-and-sorting-your-load-order/ thread.

Here a fantastic and easy to use tool to manually reorder plugins quickly.

http://yacoby.silgrad.com/MW/Mods/Reordermods.htm

The only problem with it is that it doesn't recognize plugins with the ".ESP" extension, I mean with capital letters. As for those you have to change the date in WM.

For anybody interested in including TESTools-like (based on redating selected mods relative to current system time/first selected mod timestamp) mod reordering in Mash, http://abot-morrowind.tk/index.php?option=downloads&task=info&id=17&Itemid=50 you can find a example of changes to the masher.py file to add (right click option/description):
Update time from current system time/
This command will update the time of selected files, starting from current system time, keeping the same plugin order. It cannot be undone (at least, not in a single step). It is meant to be used with files displayed in loading order. If you know what you are doing, this function is great to sort/move entire groups of files that must be loaded last, keeping the relative loading order (just ctrl+click or shift+click the files to organize).

Update Time from first selected file time/
This command will update the time of selected files, starting from the time of first selected file, keeping the same file order. It cannot be undone (at least, not in a single step). It is meant to be used with files displayed in loading order. If you know what you are doing, this function is great to sort/move entire groups of files keeping the relative loading order (just ctrl+click or shift+click the files to organize.