|Well yeah, there's no other way to connect it.|
Floppy drives have Drive Select (DS) jumpers. How you set them depends on the type of cable you're using. Floppy cables now have a 7-wire twist in them:
(where the arrow is pointing in the first picture.) When using one of those cables the drives need to be jumpered to the second DS position. Most 3.5 drives are already jumpered that way and sometimes you don't even have access to their jumper. But 5.25 drives often aren't jumpered that way as those cables weren't the standard when those drives were popular.
That's why I asked all those questions.
Anyway, assuming that's the cable you have, and the drive(s) are jumpered correctly then the one you want as drive A: goes on the end of the cable, after the 7-wire twist. A second drive (if you're using one) goes before the twist and will be Drive B:. So it'll be like this:
motherboard connection-----drive B:----7-wire twist-----drive A:
And of course the cable you use will have to have slide on connections (vs the pin connectors that 3.5 drives use). Some cables have both types so you can mix 3.5 and 5.25 drives.