Well, having the pidgen installed doesn't mean you can't use the msn messenger. It just means you have the choice to use pidgen for it. Pidgen is mainly an all in one messenger program. The getting email notifications is kind of a secondary perk. I suggested it because it is the only free one i know of that gives mail notifications for all the different popular chat clients.
Personally I would only want one program running to do the work of five. I use trillian, another multi protocol chat client, to chat on yim, msn, aim(aol) irc and icq. If I didn't use trillian or pidgen I would have to install 5 different programs to keep track of all my friends and all those email accounts.