I think I need another feat to throw two weapons at once. I had a similar question when I was using a two-weapon fighter wanting to know if I could throw two-chakrams as a full round action, but apparently rules state that when you're throwing a weapon you can only throw one thing at a time.
That being said I am carrying two bastard swords: one to throw and the other one for melee two-handed.
What exactly do you mean by throwing "one at a time"? If you have a chakram in each hand, and you have at least BAB+6, you can throw both Charkam, one as your BAB+6 iterative and the other as your BAB+1. You could also use TWF rules to throw one as an off-hand attack, though you take attack penalties in doing so. It's only if you have 3 or more iterative attacks that you'd have problems, unless you have Quick Draw or you're using thrown weapons that can normally be drawn as free actions (ie. Shuriken).
That having been said, if you have EWP for it, then you can throw a Bastard Sword in one hand, and subsequently make your attacks with the other in two hands. This does not count as two-weapon fighting so you don't even take attack penalties.