Unfortunately, the SB2000E is not capable of running at higher voltages (two or more "12vdc" rated panels in series)... Their maximum rating Voc is 30VDC.
http://www.blueskyenergyinc.com/pdf/SB2000Edatasheet.pdf
To do what you want, you need a controller that can manage a much higher Voc voltage.
And the higher priced high voltage capable MPPT controllers typically are not that efficient at lower wattages (less than, roughly, 400 watts or so)...
Check the specs. at the voltage/current/price you are interested in for the best solution (may be the SB2000E unit--don't know).
A drawback with higher input voltages is that the MPPT controllers have switching losses that increase with voltage (per Solar Guppy). It is not a lot (was it 1-2% typically?)--but it is there.
-Bill