I had started both, and when I finished getting help from the Boomers I went back to the NCR embassy and from what I could tell, the Boomers promised to help ME and not the NCR. I didn't even say to the NCR fellow (can't remember his name) that they would help the NCR, just that they would help me.

So can I continue doing the NCR missions (And maybe another factions' missions too?) while doing the Wildcard ones for the extra rewards and secretly plan for my hostile takeov- I mean.....starting up a Starbucks. Will I reach a certain point where I have to stop doing one of them?

Yes Man is always an option; part of the reason he's in the game is so you can piss off every major faction(or kill everyone you meet) and still get to the ending. Just be aware that if you turn in quests to him instead of the NCR there'll come a point where they don't let you work or them any more. Apart from that, you can work for the NCR right up until you get a pop-up warning you that you're about to hit The Point Of No Return, then go get Yes Man and finish the game with him instead.

Is there any downside to that? Do all the allies I've gotten help only me?

The allies you gain will follow you and who ever you decide to side with after you hit the "point of no return". Regardless though they will only fight by your side, I believe this is your main concern right?

Your not gonna start up the final battle and learn that all these factions that you have gained the trust of arts fighting against you. Their on your side no matter what.(for the most part)