You just need to program the .bin file to 0x0801F000
Here's how I managed it yesterday on Linux...
First, make sure the .bin file is a multiple of 8 bytes in size, otherwise you might hit the ARM boot loader bug that corrupts the last block. If it's not, somehow append four zero bytes, e.g.
truncate -s 135104 design.bin
Connect the USB cable to the more central USB port.
Put the board in DFU mode by removing the link between pins 14 and 16 then pressing reset (or power cycle).
Program the bitstream with dfu-util:
sudo dfu-util -d 0483:df11 -s 0x0801F000 -D design.bin --alt 0 -t 1024
Put the board bank in normal mode by replacing the link between pins 14 and 16 then pressing reset (or power cycle).
Your new design should now be persistent.
This should, I believe, also work with IceBoot 0.2