I found a deal with a motherboard that had a m.2 ssd with it pre-installed, that has windows on it. But it's only 250gb, and I'm planning on buying another 1tb nvme for games, and I want to put it in the top slot where the other one is, because that one has a heatsink
Adding the second SSD should not impact the first one, unless you plan on installing Windows (fresh, clean install) on the larger SSD. Otherwise, just like adding an additional SSD or HDD.
Consult your motherboard manual to make sure you know whether some SATA ports are disabled when using NVME SSDs. If so, don't try to use those ports.