This might seem like a dumb question, but if I'm using two different amps with a 990, and one has balanced inputs and the other has unbalanced, is it ok to run one amp with balanced and the other with unbalanced or do they all have to be the same?

You should be able to run a mix, but the balanced outputs have a higher gain which may cause you to apply wider adjustments to channel trims when calibrating.

So balanced inputs are better or not? I've read things both ways. Does someone have to buy both cables to determine this on their own?

Which is better is a debate that I've never seen definitively answered - and we've had a number of very knowledgeable folks weigh in on the issue around here (see the old 990 and balanced/unbalanced threads for the main examples). Balanced connections were developed for use with long cabling runs in hostile environments (recording studios, where the amount of EM and RF interference is substantial and cables had to run dozens of feet) - many people suggest that they're not needed when the run is only a meter or so in a home environment.

From the "been there, done that" camp:

The 990 zero's the left front speaker, and callibrates all of the other channels relative to that. If you run a mix of balanced and un-balanced signals (I've done it, it works fine), to get the wide adjustments required you may need to set the left front to something other than zero.

For example, lets say you run the mains balanced, and everything else un-balanced. You may find that there is a (making this up) 20db difference between the mains and sides. Auto-cal only allow +/-15db deviation from the left front; which is automatically set to zero. So, the 990 can't get enough gain for the side channels.

In this case, you would need to manually set left/right mains to (for instance) -10db, and the sides to +10db; which will get the needed 20db differential.

This can only be done in manual mode.

Re whether balanced or unbalanced preamp-amp connections are better, I've tried both (but not, obviously, in an A/B comparison) and my take is that unbalanced connections are more convenient (cable thinner and more flexible), can be cheaper ma(but not necessarily), but are very slightly inferior in performance. This is with runs of 2 meters or less. The difference I've noticed, and described elsewhere, is (certainly) reduced hum on phono using a Grado pickup (known to hum with the AR turntable) and (possibly) even more transparent bass.
This is based only on experience with the 990, nOrh Le Amp II monoblock amps, and comparing Outlaw balanced 1.2 meter interconnects with the unbalanced interconnects I was using before, which were in about the $100-for-2-meter range.
Your experience may vary.

Let me try that again without the typos.

Re whether balanced or unbalanced preamp-amp connections are better, I've tried both (but not, obviously, in an A/B comparison) and my take is that unbalanced connections are more convenient (cable thinner and more flexible), can be cheaper (but not necessarily), but are very slightly inferior in performance. This is with runs of 2 meters or less. The difference I've noticed, and described elsewhere, is (certainly) reduced hum on phono using a Grado pickup (known to hum with the AR turntable) and (possibly) even more transparent bass.
This is based only on experience with the 990, nOrh Le Amp II monoblock amps, and comparing Outlaw balanced 1.2 meter interconnects with the unbalanced interconnects I was using before, which were in about the $100-for-2-meter range.
Your experience may vary.

Sorry for all the parentheses.

To add a bit:

Balanced connections require more components in the circuit. Specifically differential amplifiers and/or transformers. Those items can add to the sound, either in a positive way or a negative way.

The only way to tell what will be better with the equipment you own is to try both and see. I've heard many reports that the Outlaw stuff tends to sound very similar between balanced and unbalanced which means they likely chose very good differential amps and/or transformers.

Balanced can give you a few more options in certain situations. Due to the differential signal, if you have a ground loop, you can cut the shield connection between two devices (referred to as a ground lift) and still get a signal connection. This can solve hum issues.

Also if you are in a situation where hum/buzz can be picked up by the cables (lots of EMI/RFI in the area, or long runs) balanced lines are much better at canceling out that noise.

I work mostly with professional equipment, which tends to be balanced. Interestingly some high end equipment comes configured with XLR line level outs which are obviously balanced, and 1/4" TS unbalanced connections. When asked why such high end equipment (several thousand dollar mic preamps) has unbalanced outputs, the manufacturers will explain it is a more purist option for those that have the luxury of short runs and want to remove the extra components from the signal chain.