I have now been using Yahoo Mail! Plus handling two separate external email account perfectly. I have mail for each account pushed to separate mail boxes on the BB thus having correct from address set when replying. All my outgoing mail is stored in the Yahoo! Mail outbox.
All it took was to add the free extra email address to Yahoo! Mail Plus, and set up BIS to get mail from both addresses as if it were separate accounts. I also had to add four filters to each of the two BIS accounts for this to work. Without the filters I would get all mail twice on my BB.
The only limitation is that BCC'ed mail comes in to the same account on the BB regardless of which address it was sent to, but that is not a problem for me.
Of course you need to have your external mail forwaded to your two (or more) Yahoo! Mail addresses (unless you are using Yahoo! Mail as your primary e-mail address).
I am so pleased with this set-up! After getting my BB I realized that it wasn't any good way to handle two accounts with pushed e-mail seamlessly without using hacks like BB-Reply. Even BES is not good for multiple accounts.
I have to say I really like BIS 2.0. With the ability to set a bit more complex filters it would be perfect. The integration of Yahoo! Mail into BIS 2.0 is a big step forward for people using BB's outside a corporate network I think.
Forgive my rant, but it just feels good to have things work like you want them to. Especially since I for a long time thought it wasn't possible. So Yahoo! and RIM when will you integrate address book sync in BIS?