I already know Im siding with Mr. House for the ending. I'm on the part where he wants me to destroy the BoS bunker. I've been doing their side quest "In the dark" completely to get to learn how to equip there armor and I want to do the same thing with the other factions as well (minus the legion). I'm just wondering if doing there faction & side quests this late will screw me over on the main story?

Do you have two quests called "Beware the Wrath of Caesar" and "Don't Tread on the Bear"? If so, then you need to reload a save before accepting the quest from House. But otherwise, I think the BOS quests are still fair game unless you destroy the bunker in the middle of one.

Doing the BoS side quest for the Power Armour training perk should not have any effect on the storylines of the other factions.
If you have the quests, Beware the Wrath of Caesar and/or Don't Tread on The Bear, active then the next House quest you do will cancel out any withstanding Legion or NCR quests leaving you with only Mr.House and Yes Man. If you report back to Mr.House or YesMan