With proper ventilation (i.e., a fan setup), you should be able to put it on its side.
This amp can be configured by adding power modules that take its output from 200 watts to 1000 watts. I don't know how your unit is fitted out -- perhaps you have it running two 200 watt modules. Given that the circuit design appears to be biased significantly into Class A operation, these amps tend to run fairly warm. The holes in the top and bottom are intended to let rising hot air flowing out the top work to suck in cool air into the bottom, in a flue-like process.
If you put the amp on its side, you will defeat this effect such that air flow will be reduced and the amp will get hotter than its designers intended -- not good. If your installation configuration dictates placing the amp on its side, I suggest you rig up a fan to force air through the holes to provide adequate ventilation. Good luck.