As far as I'm aware, this CAN'T BE DONE! It's a limitation of Android, not Themer. Android links itself to your gmail account, and it will only report unread emails in that account, not any other. The two ways around this are:
(a) forward all your non-gmail messages to your gmail account by adding your hotmail/yahoo/whatever account to gmail (you can do this within gmail on your phone, or from your PC). This is the 'elegant' solution but it does mean that ALL your emails will be a the mercy of Google
(b) as you're building your own theme, just find the simplest widget you can for yahoo/hotmail/whoever, put the widget on your homescreen and use some clever masking (such as allow overlapping widgets??) to display only the numeric character. Not sure how you'd go about changing the font size.
You might want to look at Tesla Unread
which displays unread emails on little badge icons, or browse xda's main Android forums for info on email count widgets.
BTW, I'm no expert so please don't ask me anything technical - I've just researched this problem before and I remember some of the replies I got from clever people.