The 990 doesn't do EQ - the auto setup adjusts volume levels only. Also, the 990 has a mono sub output (the two outputs are identical) so the level at the 990 is identical for both. You'll have to adjust the gain on each sub's amp to get the two matched up.

The 990 will probably set any speaker to small if it can't get down to 20Hz - your Beethovens only go about 2Hz lower than my Studio60's (28Hz vs 30Hz), but I have run my Studio60's small for a number of years now (currently using a 60Hz crossover, in fact). You can always set them to large manually and see which you prefer.