If the active subwoofer uses another line level input (for example, second set of output from the preamp), then it doesn't matter.
But in many cases, the active subwoofer uses the speaker terminal outputs of the amp (which has high DC offset versus ground) and that could cause a short to the ground depending on the design.
Only the speaker manufacturer can help you. With so many icepower based amps out there, speaker manufacturers will avoid this problem.
For example, Martin Logan upgraded the Summit speaker since Nov 2005 to allow such configuration.