You most certainly can, that's the entire point of using the Installers feature for non-esp "mods".
Wrye Mash will maintain the files in downwards order as they are listed in the Installers tab. So if you have:
1. Has file "a", "b", "c"
2. Has file "a", "d"
3. Has file "b", "d", "e"
Wrye Mash will make sure the real files in your Data Files are "c" from #1, "a" from #2, and "b", "d", and "e" from #3.
So it loads last whichever one is last in your Installers order (different than your Morrowind Mod Load Order). Details are at http://wryemusings.com/Wrye%20Mash.html#InstallersTab in the "Ordering" section, but I think what you want to know is this:
? General
? Install order is shown the table in the "Order" column.
? All packages are moved to just before the ==Last== marker when Bain first encounteres them.
? Order can be changed by right clicking on a package (or group of selected packages) and selecting "Move To". Just enter the position to which the packages should be moved. If you're moving many packages at once, they'll keep their relative order, with the "oldest" moving to the specified position, and the others following after it.
Edit: You can also look at the "Conflicts" tab for each package, which will tell you about files that it overwrites or is overwritten by, so you can make sure you are getting the order of overwriting you want.