Make sure that for some reason or another, you don't have bridge mode cables. The way you can tell, is that a normal speakon cable will only have wires on the 1+ and 1- terminals, where a bridge cable will be wired to 1+ and 2+. If you have the latter, do not use it with the speakons in the amp! You are bridging the woofer and tweeter amps, and since they are different power outputs, will hate each other . . . . violently!
Other than that, I can't think of any reason whatsoever why you couldn't use the cable either way. Heck, since you apparently have speakon on both the cabs and the amp, do yourself a favor and lose the 1/4" jacks totally, and run speakon on both ends. It will only cost you about $10, and you will be able to kiss 1/4" jack failures goodbye forever . . . . and have cables that can't get accidentally pulled out at the worst possible moment.
- Tim