phranque - 8:55 am on Sep 11, 2012 (gmt 0)

you use the same DNS for all the subdomains of your domain and for all protocols.

the 2nd hosting configuration should only receive traffic for subdomain.example.com and it can be configured for that specific subdomain or for wildcard subdomains.
if you have it configured to accept requests for wildcard subdomains, make sure you have sufficient hostname canonicalization redirects in place.