Ever since they switched stuff around between 1.3 beta and 1.3 I've done that a time or two myself.
I'm not sure what you're asking on that though - it's the multiple instances Mozilla won't allow. Is opening new windows from the initial instance not doable for you? Then you could just send them to different desktops. Or try this:
mozilla -remote "openurl(http://www.foo.com,
in an xterm. You might be able to write a shell script with half a dozen addresses, or maybe just 'about
:blank' or something to get them started. Then invoke that instead of 'mozilla'. Just exec a normal mozilla first. Maybe something like that.