If the drive is plugged into the last socket on an IDE cable it's better to set the jumper to master, that way if you get another drive you can set the jumper on it to slave and plug it into the middle socket without having to adjust the existing drive jumper.
If the motherboard has both SATA and IDE sockets then how can it be bad to use both? I don't have a system that runs SATA drives yet, but I was planning to use the IDE drives from my old system in the new one I'm waiting on arriving. The motherboard manual states it has 6 SATA sockets and 1 PRI-IDE socket which means I can use 2 IDE devices. As long as it's used as a data drive there shouldn't be a problem.
The only problem I know of with SATA drives is the driver issue when installing windows without a floppy drive, as windows doesn't have SATA drivers incorperated you have to install them from floppy before windows will install on a machine with a SATA drive as the boot device, that and installing the OS onto the SATA drive before installing the other IDE drives in order not to confuse windows as to which is the boot drive, if you already have windows installed to a SATA drive there shouldn't be a problem adding an IDE drive at all.