converting existing single installs to multisite/subdomains

this is for andrea_r mainly because I asked her, but will take any help: I’ve been using WP since late 2007 and have done a lot of learning along the way. I’ve got WP as my main site, plus a client area in a subdomain as a separate install, and now have a handful of individual installs for client dev sites. If I were starting today, I think it would be pretty straightforward that I would want to set up a multisite install to handle all of this better, but I’m a little concerned that if I try to convert everything at this point, it might be messy.

I want to keep things in subdomains, but can I set up WP to use subdomains if they already exist with sites? Do I have to back those sites up/export them and take them down before I convert them? Or is there a better way to convert them?

Also, I have a totally separate software package running in a subfolder of one of the subdomains; can I still use that somehow, since the new subdomain would be virtual and all? Or what do I do instead?

Thanks in advance for your help.