Aligning in Maxim
I got this answer from a support ticket from Maxim. This is in answer to the question of whether Maxim resamples the data when using the "1 star method" with or without "Use Centroid".
The "Use Centroid" option for Manual 1-star alignment simply adjusts your clicked point of reference in the image to lock on to the nearest (brightest) centroid. This is done to ensure maximum accuracy in the alignment process. If you leave "Use Centroid" unchecked, it will simply take the points you provided in each image without adjustment for objects in the image. Regardless of this option, the alignment is calculated at the sub-pixel level, and the image is resampled using either bilinear, or bicubic interpolation (depending on which method you specified in the options menu).
I would advise not aligning images prior to photometry if you can avoid it, since the auto-matching tool in the Photometry suite has some object detection built in — but if you must align the images, using bilinear interpolation will help minimize the smearing from the resampling process.
Sorry for the bad news. This just goes to show you that there are no stupic questions.