[Exim] Queue runner routing question

I am using exim as a mail gateway that mainly routes mail for different
domains. For various reasons, I would like to have exim listening on two
different ports (25 and 1225); each port would correspond to a different
configuration file which routes several of the same domains differently.

I have this setup currently working, but I have a question on how mail gets
routed that falls into the queue. My understanding is that every time a
queue runner starts, it goes through the rules again to determine the route
to take for each message. Is it smart enough to know which configuration
file each email originally used (the way I hope it works), or does it
default to the standard /etc/exim.conf?

Thank you,

Michael Graf