If your organization, school, or company has volume licensing for FileMaker Pro and want to make your package Munki-able, this is how you do it (based on Assisted install for FileMaker Pro and FileMaker Pro Advanced).
Find your FileMaker installer .mpkg file. This installer file will likely come on a read-only medium (read-only .dmg or actual physical CD/DVD), so drag it to a temporary read/write location (e.g., your desktop).
Add in or change an options as you see fit (you don't need quotation marks around anything—just put the text for AI_USERNAME, AI_ORGANIZATION, and AI_LICENSEKEY after the equal sign on each line). For other options, 0 means No and 1 means Yes.
When you're done, close and save the file.
Next, just go ahead and import that modified .mpkg file into Munki (e.g., munkiimport FileMaker Pro ## Advanced.mpkg). The Munki import process will create a read-only .dmg container for the .mpkg file.
I'd recommend using an installs array (/usr/local/munki/makepkginfo -f) based off the info.plist instead of the FileMaker bundle. For example:
<string>/Applications/FileMaker Pro 13 Advanced/FileMaker Pro Advanced.app/Contents/Info.plist</string>
I've found using an installs array based on the bundle will make Munki think FileMaker 12 is installed if 13 is. If you use multiple versions of FileMaker simultaneously, you'll definitely want Munki to differentiate among those versions.