The TemplateID is a special field in FAST, but all the other fields of a FAST message are treated equally. FAST does not "know" about the structure of a FIX message (beyond what the template tells it)
The fields in the FIX header and trailer on a FAST encoded message are handled just like any other fields -- define them in the template and provide values to the the encoder for those fields. There are, however, two fields that can cause problems: message length in the header and checksum in the trailer.
These two fields are left over from encoding FIX messages as simple character strings. They are not particularly meaningful for a FAST encoded message since the number of bytes and the actual contents of those bytes might vary, so it is possible that you and your counterparty can agree to ignore the contents of these fields.
If not, however, you may have to produce a temporary FIX/text representation of the message so you can obtain values for these fields to use during the actual FAST encoding. Unfortunately QuickFAST does not currently help with this.
Dale