My experience with loading for an amphibious assault is that you be well advised to create separate TFs during loading with one TF loading all your assault units on APAs and any non assault units loading onto APs in a separate TF.
Yeah, that is what I have been doing. Using an AP per division would get a lot more troops. Just trying to see if I can maximize the landing. Gonna have to put the SeaBees and Base forces on the APs like my original idea. I can underload the APs with what can unload in a day, maybe. I am used to having a lot of extra space even on the APAs. Might have to see how close I can get to maxing them out.