Air system with multiple filters

If you have 2 filters racks in your system you could just pick the easiest one to change and ues it exclusively. You could also use both and change the second one less often. That seems like a lot of monitoring. You may have to check both often at first until you are able to determine a schedule. It's not a bad idea but in most cases that level of filtration isn't required.

Filtering the return air at the point of ingress is by far the best option. That way there is no dirt accumulating in the return ducts and you can readily see the condition of the filter.

I removed my internal filter and put in a surface mount 20x20 Merv13 on top of the former return grill which I also removed. It's a vertical configuration and it's protected from anything falling on it, kicking it, etc. The grill just reduced the air flow and was a dirt magnet itself.