Sign yourself into a home for the bewildered :-)).
Seriously, you can probably do it but I imagine qmail can handle more than one domain. I messed with it about 10 years back, and it messed with me more than I messed with it. Then I discovered
http://www.lifewithqmail.org
Linuxfromscratch do/used to do a thing on compiling it with options which allowed you to move it to sensible places. But it uses variables, groups and lusers so it's a job of work(Patching) to put 2 different installations in.
Are you not able to use numerous domains on the one server?