I have the following under the seat, all held by the built-in pair of interlocking rubber straps:
Heavy duty ziploc bag #1:
User manual in its vinyl envelope
Proof of insurance
Heavy duty ziploc bag #2:
BMW "extension" tool set, part number 71-60-7-704-086
The heavy duty ziploc bags have worked very well over many years, to keep motorcycle paperwork from becoming wet, discolored, rotten, or brittle. The plastic is much thicker than a standard ziploc bag, and the bags have multiple "zips" at the top.
Even though the toolkit comes with its own roll-up pouch, the 2nd ziploc bag ensures that the small torx bits don't fall out (which could easily happen), and it serves as a spare in case I need an extra bag for a greasy part or something. See this thread for pictures of the toolkit: http://www.i-bmw.com/showthread.php?t=5060
The interlocking rubber straps and the plastic "stops" under the seat are a perfect fit for the manual, or manual + toolkit. I have a late production 2007 K1200GT. The 2006 and early 2007 K1200GTs have a different seat. I don't know if those earlier seats have the same features.