Best dedicated server setup for WPMU with domain mapping

Yesterday I signed up with WPMUdev and am incredibly excited to use the Multi-site plugins...I was hoping you could look at my situation and let me know if there is a better way to setup the dedicated server I am thinking about getting or if there should be no problems. Here is my situation.

I currently run a company called http://www.shirtandsimple.com - this site is broken down into different locations (or instances of the site) so that when a user visits the website, they pick which location they want to order from and then they are taken to a fully customized website for that location (so like http://www.shirtandsimple.com/hawkeys or http://www.shirtandsimple.com/madison or http://www.shirtandsimple.com/olympia). We have recently made the decision to move this network of sites over to WP multi-site so each location can be better customized, organized, and utilized. I have decided to move from my shared hosting plan to a dedicated server because of this. I have purchased a membership at https://premium.wpmudev.org and plan to utilize many of you plugins and features. One of these is a domain mapping feature that claims to allow me to offer different domains to users or let them use their own domain (https://premium.wpmudev.org/project/multi-domains and https://premium.wpmudev.org/project/domain-mapping). Therefore, instead of being http://www.shirtandsimple.com/olympia - this location could be http://www.bolandersigncompany.com and therefore be completely branded from their parent company.

The other thing I'd like to do is merge some of the sites I have floating around the internet (some on various shared hosts and one on a VPS host) to my new dedicated server. This will save me some money and hopefully improve the speed of my sites.

However - I talked to my current host today and he said there might be problems with the domain mapping for my shirtandsimple.com multi-site if I have any other sites on the server. They said if I only have the shirtandsimple.com site on the server that any other sites/domains pointing to the server will be easier to assign to one of the shirt and simple multi-site locations. He says that if there are other sites on my server, it will be complicated to achieve this domain mapping I'd like to have.

I'd really like to be able to offer all my sites on the one server but the shirtandsimple.com network is most important and I was really hoping to have the domain mapping work. Will domain mapping work if there is more than one root site on the dedicated server? I have limited server configuration knowledge so I can't do a lot of advanced setup (and would prefer not to have to pay every time I add a new location). Is there a way I can do this?

Thanks so much for your help!