Hi David! This is Megan from SEOmoz. You could really set up your campaigns either individually or as a root domain - it just depends on what you think would work best for your needs. Here are some pros and cons, though, that will hopefully help you reach your decision. 
Root Domain -
Pros: 1. Might be easier for you to have everything in one spot rather than clicking between campaigns. 2. If you have the same keyword you want to track for everything then you would only need to enter it once as opposed to adding it to each campaign (and thus taking up several keyword spaces out of your allotted 300 instead of just 1)
Cons: 1. You're only given 3 competitor comparisons, so it would be pretty limiting if you have several competitors you want to track against
Individual campaigns -
Pros: 1. You can track up to 3 competitors for each campaign so you would be able to keep an eye on the direct competitors for each service. 2. It might be more convenient to have all of the data separated out to create clear lines between the services.
Cons: 2. It would takes up a lot more campaigns slots
I hope this helps at least a little bit! If you want to send us your specific URLs so we can take a closer look, feel free to send them to help[at]seomoz.org.
Thanks!