Try this: Say you have three images, one of which is going to be your background and two of which are foreground elements with alpha channels. We'll call these Background, Foreground1, and Foreground2. In the Foreground1 image, duplicate the one existing layer then select the lower of the two layers. In the Background image, Select - All and Edit - Copy. Back to Foreground1: Edit - Paste. Foreground1 should now have three layers; from the top: A copy of the Foreground1 image, a copy of the Background image, and the original Foreground1 image. Go to the Foreground2 image, Select - All and Edit - Copy. Go back to Foreground1. Click on the top layer, then Edit - Paste. You now have both Foreground images on top of the Background image on top of the original Foreground1 image. Go back to Foreground2. Click the Channels tab, then click the Alpha 1 channel. Select - All and Edit - Copy. Go to the Foreground1 image. Click on the Channels tab. Click on the Create New Channel icon. Edit - Paste. Your Foreground1 image now has 4 layers: Foreground2, Foreground1, Background, and the original Foreground1. It also has 6 channels: RGB, Reg, Green, Blue, Alpha1, and Alpha2. You can close the Background and Foreground2 images; everything is in the Foreground1 image, all registered. You can do whatever you want now. I would suggest rather than blending layers together, you simply cut each of them out by Select - Load Selection - Alpha X, Select - Invert, and Clear. It's also easier to just Select - Load Selection - Alpha1, then Edit - Copy from each image and paste onto your background. The only problem with this is that the pasted images may not be in registration with each other.

Annie