Is there an easy way to level a board to be used as my waste area, ie, make a square and tell it to fill cut or just free hand the router on the gimbal?
As Bob said (besides NEVER!) just make a large square and fill cut in small amounts.
Set your probe height to what you guess is the highest part of your board. and shave a 1/64 - 1/32 off and see how it looks.
I used this on mine, but any large mortising bit will do.
It will also show if your router is not perpendicular (you will get a pattern on your waste board).
…also set step-over to 80-90% vs the default 40% 
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I would look at this tool from Magnate
If I am not mistaken this along with the other bottom cleaning bits that they sell are the only truly flat bits on the market
if you had a 1/2" shank router CMT sells a excellent insert tool for spoilboards I use that one and its amazing
spoilboard surfacing bit is not one that you want to cheap out on
also I would stick around 50% or less stepover to avoid lines and I would also look at tramming your spindle in while your surface your work area
I wondered, do you trammel before or after leveling?
you usually surface the board then tram the spindle and then surface the spoilboard a second time
That makes sense.