for some reason i can't complete the brotherhood quest for the air-filtration, after the new commander is in power. i have all of the needed components, but can't turn them in to finish the quest. should i have not allowed the new commander(white dude.i forget his name) to take command, and turned the items in to the original commander?(black dude)

If Lorenzo is the one not taking the filters & you have EDE with you/have been working on/completed EDE's quest, try firing EDE and talking to Lorenzo again.

Otherwise...the filter & leader quests supposedly can get linked in such a way that yes, you can't do one before the other. I have no experience with it myself tho so not sure how/don't understand how that works. I'd suggest looking at the http://fallout.wikia.com/wiki/Still_in_the_Darkfor this quest and reading the bug notes at the bottom of the page.

k, thx. i didn't know about the bug notes.