So I got the Battle at Bunker Hill quest from Father at the Institute, and I decided it was time to break and run from them. Whoever Father may have been, he's not a son of mine. He's a child of the Institute.

So I was weighing my options between the Railroad and Brotherhood. I've actually never been back to the the Police Station after completing Danse's initial quest. I get to the station, and the Knight out front remarks "If you aren't Brotherhood, you're nobody.", well that pretty much threw me into the arms of the Railroad. Right after the welcome speech, Des gives me the whole run down about being at the Institute, and how I ought to side with the Railroad over the Minutemen.

My question is....does it matter who I choose to side with here? The Minutemen are my boys, and I'll definitely fight to liberate any Synths I can in the process, but I ran through the dialogue of both, and Patriot could be a major help down the line. But I also know for a fact I want the Minutemen in the forefront.

Can I tell Des I'll support her to get Patriot and not irritating the Minutemen?

I think if you tell her that you'll side with the railroad, you get locked into the railroad ending and can't do the minuteman one. It might still be possible to do the minuteman ending if you betray the railroad and make them enemies, however.

There is an "unsure" option, I'd go with that if you aren't sure yet.