I've got an Autocom setup that I use for pillion, bike to bike, GPS, MP3 and phone in partnership with a Zumo 550 GPS on the handlebars.
The Active Rider Autocom that I've got fits nicely behind the battery box under the seat. There's not a lot of room but I can coil up the spare cables that I'm not using (e.g. the pillion cable if I'm on my own) in the same space behind the battery, pulling the rubber battery strap over the top to keep everything in place.
I've wired the Active Rider in permanently using the accessory plugs that are meant for the optional accessory socket. I was careful to wire the Zumo to the same +ive and -ive connection to avoid ground loop isolation issues that some of my friends have had with car installations.
My helmet is an Arai Astro in which I've fitted the speakers behind the fabric in the ear recesses. As others have said, getting the positioning of the ear pieces is very important. It took a while for me to find the sweetspots but now I'm able to ride along listening to music at 70 mph with the visor open a little bit to let air in and able to listen to the music whilst wearing foam ear plugs.
The one thing that I will say is that it can quickly get expensive! Autocom charge an arm and a leg for the accessory leads.