Not sure what kind of track you have. If not FasTrack then you can mount the the IR board separately on the track with the new cataloged items. I am an S gauge operator and Lionel does not make S gauge sensor tracks. The layout was built before the new separate boards were available. We bought O gauge FasTrack Sensor tracks and removed the two boards. We custom made connecting cables to put the programming board some distance from the actual sensor location. Here are some pictures just in case this gives you any ideas for your layout.
The black wires are the DB9 LCS cables, the blue wires are the connection between the sensor and programming boards.
The first picture is one of the Sensor tracks as installed in the layout. The second is the appearance for the underside. The plywood top of the layout was cut out under the circuit board. The third is the programming board, it is under the fascia edge of the layout, easy to reach.