There are multiple issues here.
First, if you want to use both floppy drives, your floppy cable must
have both connections on it, since there is rarely more than a single
floppy controller slot on a motherboard.
Second, there needs to be 5 (if I remember correctly) pins reversed
between drive A: and drive B:. Most floppy cables already have this
reversal.
Next, if you're using 5.25 floppies, you must remember that the 1.2MB
drives have smaller read heads than the 360KB drives, this means that a
1.2 drive will have no trouble reading a 360 disk, since the tracks are
wider, and the smaller heads are (usually) in the middle of the 360KB track.
However, the 1.2MB tracks are smaller, and any kind of misalignment
means your 1.2MB floppy drive may not read the disks, because of this
factor.
I had many many 1.2MB disks not work in one machine, but work fine in
another one, while all 360KB disks worked no matter the drive.
Plus, as you may or may not already know, sometimes, hardware will
determine which drive letter a drive tries to be. Most of the floppy
drives had physical jumpers you needed to set to determine their drive
letter, though depending on how old your drive is, (or newer depending
on how you look at it), there may not be jumpers, and the cable
determines which drive is which.
You shouldn't need to disconnect either of the drives, the one at the
end of the cable will usually be A:, while the one in the middle will
usually be B:. That is of course subject to cmos settings, jumpers, and
cables, but generally things just work when everything is configured
properly, and/or if the drives don't have jumpers.
This same sort of thing goes for MFM HDS too, only those have separate
control 20-pin cables that must be present as well.
Sometimes, I have to wonder why there's less room inside modern pcs,
even though there's fewer cables.
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