No sweat. We do that now, at Heroku. We happen to use Godaddy for the domain registrar, but any DNS control panel will let you do the same thing.
The other explanations I read here are a little general, here are the specifics...
The explanation at heroku is very good, at : http://docs.heroku.com/custom-domains
(there's even a very good screencast shows step by step)
the key thing is if your ROOT domain (mycoolsite.com) is at Heroku you want to create THREE "A" records, because they do some fault-tolerant crossover magic. So you'd have an A record for
75.101.163.44
75.101.145.87
174.129.212.2
Now for each subdomain you create a CNAME record
www -> proxy.heroku.com
client1 -> proxy.heroku.com
client2 -> proxy.heroku.com
client3 -> proxy.heroku.com
NOW on the HEROKu side, you have two apps right? The 'brochure app' and the saas app.
Login, and for each app go to Resources -> Addon -> Get More Addons ->Custom Domains (free)
for the brochure app, add ONE domain: www.mycoolsite.com
for the saas app, add each of the clients, eg:
client1.mycoolsite.com
client2.mycoolsite.com
client3.mycoolsite.com
That's it. works like a champ. Have fun.
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