how to trigger my sub amp when main powers up.

If your trying to get the remote to learn the power button for the other, you may have to program to a button other than a power button. A lot of learning remotes don't learn the power on/off on the same power button itself. I'm assuming this is what your trying to do since they're both remote receivers. If it doesn't work, you may have to use both remotes. The subs must be easy to drive if your using a receiver to do that. Page 26(AVR3600) may help for learning the other remote codes. Its surprising they both don't turn on with the remote. [http://www.harmankardon.com/resources/Brands/harmankardon/Products/ProductRelatedDocuments/en-US/OwnersManual/AVR_3600_Owners_Manual_Eng.pdf][http://www.harmankardon.com/resources/Brands/harmankardon/Products/ProductRelatedDocuments/en-US/OwnersManual/HK_3490_OWNERS_MANUAL.pdf]

Dont most subs "wake up" when a music signal is sent? Just leave them on is also what most do.

So if I understand, you are using an AVR to power the satellite section of your main speakers. Then you are using the left/right main out of the AVR to the preamp inputs of a 2 channel receiver to power the passive woofer section of your mains. Is that correct or not? I am not too familiar with the remote you use with your pieces, but many can be taught those commands. If your remote is not capable of learning there are those that can have unit codes entered into them and be taught macros allowing everything to be powered up with one button. Harmon should be able to get you the codes to program in to the remote. I believe Logitech has universal remotes that will do this if yours won't.

Csm, if they were passive then the AVR would power them and he wouldnt need to power them.
I still am confused about a powered sub , right? That doesnt wake up when it recieves a signal.

From his description, I don't believe the subs are powered. He states that he is using a HK3490 to power the subs in his main speakers. The HK3490 is a 2 channel receiver. It sounds as if he is trying to biamp his mains using both the AVR and the amp section of a different receiver (the 3490). It also seems he wants both receivers to power up with the push of one button. It would be helpful if he would clear this point up and give some more detail about his set up.