We use FV2 on both Mountain Lion and Yosemite throughout our organization. One of the biggest things that you need to be sure to do in order to have a successful deployment is to make sure that your management account is enabled for FV2, as the JSS relies on that account being FV2 enabled to do things like automatically re-issue a recovery key to machines which either have "invalid" or "unkown" key statuses. You can have the JSS enable for only management user when you apply the FV2 config, we just haven't gone that route yet.
I would use the JSS built-in FV2 configuration tool set paired with either a push policy or a Self Service based policy to kick the config out. You can do the FV2 enablement via Config Profile, but JAMF has an open bug or two on that front, so we haven't gone that route either. There is a custom config profile out there which disables the users ability to go into Sys Pref - Security - FV and turn off FV which we are experimenting with...
One last thing - make smart groups based on FV2 statuses - we have a set of notification only (green, yellow, red caution style icons) policies which are featured in Self Service that display the current FV2 status to the user. FileVault is on, FileVault is off, FileVault is deferred, etc.
