I keep mine under the trunk. It doesn't pick up there, but I really don't care. In Texas, if they don't pick up your toll tag, the system compares the picture of your license plate - and if it is registered to a toll tag, it just hits your account as if the tag was read.
If they can't come up with a tag that works on motocycles, shame on them.
If it senses then that's fine and if it doesn't then then look up my license # and just add it to my bill.
A nice HPD rider showed me that 'riding the line' through toll plazas results in a free trip most of the time. However, if the sensors pick you up and you don't have an EZ Tag then they add on few mor dollars to your trip.
IMNSHO, bikes should get a discounted rate on the tolls since they don't cause as much wear on the roadway as what cages and other larger vehicles do.
I have mine (the old thick kind) in the right fairing pocket. Works good (although I think the battery is getting weak).