A couple different ways.
I have location fences along X0 and Y0, and use cam clamps to hold my parts against the fences.
I home the machine before machineing the fences, so they are at machine zero.
I just turn on the machine, home it, place the part against the fence, and cut.
I also have threaded inserts in my table, and a layout of the holes in my drawing template. So I can also bolt parts to the table through holes, and know exactly where they are on the table. (I'll first use the fences to drill mounting holes in the stock)
On our work machine, we have pop up pins to locate sheets.
It's a 5x12 table, and I also engrave a 4x8 outline, and use that to locate smaller parts.
If I need precise locations, I'll place a sheet on the vacuum table, and route a fence in it to locate parts. I don't turn the vacuum off until I finish, which can make it difficult to remove parts.