Creating Flash Videos with H.264

I am running Acrobat Pro 9 on my Windows 7. I created embedded video clips and save it as PDF files which I put into code through FLV. Lately, I’ve been talking a lot about having Flash on my iPad and wonder what if I embed the video as H.264 as an alternative to FLV. I initializes a test video and gather all to H.264 and utilized it with  Roxio Copy and Xvid4PSP. I am done with the testing but the dialog box is still showing, Your file will be converted. There is no check box for “maintain H.264 encoding”.  My question now is since there is no checkbox present, does it mean that my videos are not amenable? Or I made an error when I install Acrobat? Do I need any graphical changes in the H.264 controls? How can I tell if those videos are already converted to Flash? Which among FLV and H.264 is best to use? I need your knowledge on this, so anyone please help me. Thank you.