Right now, the social modules use the app page ID for grabbing their data. We'll be adding a parameter to the modules to allow you to override this value with a different one (for a separate page, for example) soon. We wish Facebook would let users combine Apps and Pages, in all honesty, but they're somewhat separate in Facebook's eyes.
If you'd like to add this manually until we add the parameter, and you're comfortable modifying a line of code, you can edit the following file:
/modules/mod_jfbcfan/tmpl/default.php
On line 25, update the beginning of the line with your Page's ID, by hard-coding the profile_id variable like so:
<fb:like-box profile_id="123456" width="
Replace 123456 with your Fan Page ID. If you choose to do this, please let us know how it goes. We haven't tested this yet, so would love to hear your results.
Thanks!