Well, I've really hacked this around, but I believe I have a workable solution. I now have my SME Server v5.6 connecting to easydns and updating both of my domains. (1 primary, and 1 virtual)
Basically, I've duplicated all of the easydns/ez-ipupdate service to run as another service called easydns1.
Here's a quick run-down of what I did.
1. Copy /etc/easydns.conf to /etc/easydns1.conf making appropriate changes to easydns1.conf for your 2nd domains
2. Copy /sbin/e-smith/dynamic-dns/easydns to /sbin/e-smith/dynamic-dns/easydns1. There are several changes to make in this file, outlined in the next couple of steps.
2a. Comment out the line that expands the easydns.conf template by putting a # at the beginning
2b. In the "EASYDNS=" line, change "ez-ipupdate" to "ez-ipupdate1", and "easydns.conf" to "easydns1.conf", and "easydns.log" to "easydns1.log"
2c. In the "if" statement under "STATUS=offline", change "easydns.log" to "easydns1.log"
2d. In the rest of the file, change "ez-ipupdate" to "ez-ipupdate1" every time you see it. There are several.
2e. Exit and save your changes
3. Copy /usr/local/bin/ez-ipupdate to /usr/local/bin/ez-ipupdate1
4. Start the service. "/sbin/e-smith/dynamic-dns/easydns1 start"
5. Check /var/log/messages to see if it worked. "tail /var/log/messages"
6. If it worked, setup the startup script so that it will start on boot.
6a. "cd /etc/rc.d/rc7.d" then " ln -s /sbin/e-smith/dynamic-dns/easydns1 S99easydns1"
6b. If you do an "ll" in /etc/rc.d/rc7.d, you should see S99easydns and S99easydns1 both pointing to their respective files in /sbin/e-smith/dynamic-dns/*
That's it.

Good Luck.