The fines will end up in the filter pretty much whether the filter is above, or below, the blower. Adding a clean-out at the bottom would allow you to use compressed air to clean the filter, and allow the dust to settle into the cleanout. The only problem I see, though, is that any hole you'd put in the end of the filter would likely create a ledge, where most of the debris would accumulate (instead of falling into the cleanout).
Making the filter easily removable so it can be taken outside (for cleaning) may be a better long-term solution.
Making the filter easily removable so it can be taken outside (for cleaning) may be a better long-term solution.