Render the 3d and live acton separetly from after effects and composite them in premiere. Export the the 3d footage as a quicktime file but make sure it's exported using the 'millions of colours +' option. The '+' is very important, it's the alpha channel. Another problem could be that your image sequence compostion is set to 30fps and you footage is 25fps or vice versa, you can easily change it in file>preferences>still image, i think?