Stacking several smaller air filters on top of each other to place them on a larger air controller is not recommended. Doing so can cause costly damage to the air conditioning unit, as residential ovens are not equipped to withstand this level of air flow restriction. It is better to use just one filter, such as a two-inch filter, and change it as needed. In some cases, the air controller's intake grilles or ventilation grilles have a filter depth greater than one inch.
It is not recommended to place 1-inch air filters to fit in a 2-, 3-, or 4-inch air filter slot. Doing so will make the fan work harder (more air restriction) and reduce efficiency. Adding an additional filter would make them even more so, unless the other filter was removed and the new one was less restrictive. Having multiple return grilles solves this problem, but it also requires air filters in each vent to properly filter the air and prevent particles from entering the fan motor.
Because air controller filters have more filter material because they are larger, they can collect and retain more dust, pollen and smoke before they need to be replaced. Medium-grade passive filters are much better than a cheap disposable filter, but not as good as a pleated filter. The type of filter your system can use depends largely on the duct system, but if you have used the Filtrete filters without problems, NaturalAire filters can also be used. When it is time to change your air filters, it is best to replace them with last-line permanent filters which are roughly replacements for a cheap filter, as they filter out birds and small children.
The best way to prevent dust from accumulating on the air conditioner intake vent cover is to replace air filters regularly.