There are a few different ways to do this. This is one of my earlier boa setups and the cage is similar in size to your cage.
48 x 24 x 14.
The heat panel is on the left and is about 6 inches out from the left wall and centered.
The Pro-Products guy recommended I put the probe on the opposite side of the cage. I came in through the vent in the back and stapled (use carpenter staples) it to the ceiling so if dangles just off the floor. (you can see it on the right side) I set the Herpstat at my ambient temp and the hot side just happens to be in the right area. So a cool side temp of 83 is 91-93 on the warm side.
You can barley see it here but it comes in through the back right vent. I believe AP has rear and side vents? Also, a small hole is no big deal.
I use that method in all of my cages.
There are others who do the opposite and have the probe right by the panel and also have success.