Q: How do Rapid Shot and Two Weapon Fighting interact when dual-wielding thrown weapons?

In this circumstance, Rapid Shot adds to your primary hand attacks only. So if you have RS1 and TWF1, and BAB+6, you could combine the two in a full attack to get 3 attacks with your primary hand (two from BAB, one from RS) and one with your secondary hand (TWF), provided at least one of your primary hand attacks was to throw the dagger (or whatever thrown weapon you had). Note that unless you have Quick Draw, you can only make one such thrown attack in your action and that any attacks you make after it would be unarmed strikes (there's nothing to stop you throwing the weapon as your last primary hand attack though). With Quick Draw, you can mix melee and thrown attacks in any combination for as long as you have weapons to throw.