If you're only using DOS2/2.5 you can have 4 drives D1:,D2:,D3:,D4:. You can use the shortcut D: to refer to D1.
D1 is the boot drive, if you want to boot a game, power off the atari, put the disk in D1, power on the atari holding down the option key (if you are on an XL/XE machine) to turn off BASIC and it will boot the game.
If you need to swap disks, do that in RespecQT
Remember that the files you see on your PC, the atr files themselves are actually usually disk sides, not always multiple disks. most games came as a single disk, some bigger games required you to turn the disk over and load side 2, really big games had a second disk to give you sides 3 and 4 so putting atr 2 into disk 1 is actually the same as turning the disk over, you couldn't put two sides of the same disk into two different drives so most games didn't support multiple disk drives. If a game saves your position you would usually put that disk in D1 if a second disk drive was supported.
Drives above D2 are really for more serious work, where you need lots of space.