The simple answer is "yes". The BCS is pretty easy to customize to do just about anything you need. It would be no problem to turn both elements on, and then switch to just one element once you've reached optimal temp. Float switches could be wired into SSRs, or could be monitored by the BCS and used to cancel or temporarily halt a state.
Others on HBT have better write-ups, but basically the BCS is a state machine. A state could be a number of things that happen simultaneously during a brewing step. For example, your heating your HLT to 168 (both elements on), pump is recirculating, etc. You simply tell the BCS that when the HLT gets to 168 you want to move to a new step. The new step shuts off the big element, and uses the 3500W element to hold temp. You can hold temp using a PID loop, or simply hysteresis. Lots of options built-in. Combine steps together and you have a process. I use a single process for brewing, and others for fermentation control. Each process can have up to 8 independent steps. . . . the possibilities are pretty much endless, and I don't think I can do the system justice. . .