Tvheadend takes it information about muxes directly from the central repository of the dvb-apps utils. Each time a new official build is created, the latest set of initial scanning files is taken from there and converted into information that tvheadend then incorporates into it's binary. The program that actually is doing that transformation can be found in the src/muxbuilder directory in the tvheadend source code.
You can find the latest set of initial scanning files here:
http://linuxtv.org/hg/dvb-apps/file/5e68946b0e0d/util/scan
for the US you need to look into the atsc directory I assume.
If the frequencies that you need are not listed there you can send an email to the linux-media mailinglist with an updated version of the file. Then the maintainers of these files can update the required files. You can also update the file your self, run muxbuilder and then compile tvheadend from source.
There is also issue number #72 which asks to be able to specify/import these files directly instead of making them hardcoded into tvheadend.