I'm running Starcraft via Wine. It runs perfectly, but I don't know how to add an entry to the list of servers. In Windows it's added via reg file.
Starting regedit is
In regedit I have a key called "battle.net gateways" in: HKEY_CURRENT_USER\Software\Battle.net\Configuration
I hope that is of help.
Another place where you could start looking for the correct place in the registry is iCCup.com. ICCup is a ladder for broodwar that has its own ladder server (that has to be configured in the registry).
Playonlinux supports a Regedit application, meaning you would have to tweak the registry manually.
You can find Playonlinux in the Software Center.