"Service Menu" --> "LinHES Configuration" --> "Remotes" then select your remote and press "Next" and "Finish".
If your remote is not listed in the menus you will have to set it up manually.
In LinHES LIRC is started by runit. LinHES does not have a hardware.conf file for LIRC but instead uses the runit run script at /etc/sv/lircd/run to configure and start LIRC. If your remote is not starting you can put the commands to start your remote in /etc/runit/lirc.sh. Make sure to use the lircd -n switch to keep lircd in the foreground as runit requires the processes it manages be in the foreground.
Next you will need to create a directory in ~/remotes/ for your remote and copy in the lircrc, lircd.conf and picture file of the remote. The picture is not required but if you have one it will display in "Service Menu" --> "LinHES Configuration" --> "Remotes".
If your remote is not included with LinHES please open a ticket and attach the files you created to make it work so that it can be included in a future version of LinHES.
A very detailed guide filled with lots of information to help you debug your remote under LIRC >= 0.9.0 is posted here.
If your remote is included with LinHES and you have modified either the /etc/lircd.conf or /etc/lircrc files your changes will be overwritten the next time the LIRC templates are updated or a different remote is selected from the Services Menu. The easiest way to avoid losing your modifications is to make your own remote in ~/remotes/YourRemoteName/ and copy in the lircrc, lircd.conf and picture file of the remote. Your remote will be available as an option in "Service Menu" --> "LinHES Configuration" --> "Remotes". and it will not be overwritten by any updates. If your remote has the same name as a remote in /usr/MythVantage/templates/remotes/ both will show in the UI. However, when either UI item is selected only the files in ~/remotes/ will used.