12tree, those clips are actually helmet clips! Yeah, I know, go figure....
But there are a few posts & a coupla threads here showing how you can fairly easily make an extension clip that won't rip the tupperware &/or paintwork so you can use them to hold your helmet/s.
As for the 'trays', the little depression under the pillion seat RH side rear mates with the cut-out in the seat pan & is intended to fit the OE tool roll, which is meant to strap (with a velcro strap) up into the seat pan cut-out. The LHS rear flat area covers what was the battery niche on the 2012 & earlier Spyders, mating up with the box shaped impression in the top front inboard corner of the LH Pannier that still exists. Altho since the 2013 RT & on, that space has only housed a couple of relays & connectors that can easily be moved out of the way if you want to drop a little case into that space & convert the top placcy cover into a flap/lid, like some of us have done!
The flat areas underneath the riders seat seem to be pretty important to moving airflow thru & then out of the engine compartment, so fill them with 'heat sensitive' &/or enough material to block that airflow at your peril. Do you really need to ask me how I discovered that??!
I made a couple of loops (see the picture) to give some extension for the helmet D-ring when I really feel a need to lock them up and have no available storage compartment space.
Under seat
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Originally Posted by 12tree
Yeah, I know, go figure.... 
