I use mobileme email, plus I have several pop emails with my ISP etc.
The way I've made it all work transparently for several years now is thus..
I went into the email settings of each POP account, set it to forward all messages to my mobileme email account, once this was working I went into the Mac mail preferences on my computer and turned off the pop accounts, so there is only my mobileme account receiving and sending all messages.
This works well for me, I can receive all messages from all accounts on my iPod Touch, and when I get my iPad it will work also.
BTW, I have 3 mobileme mail aliases, and my Ipod touch has no problem handling them.