@pecan Thank you for that detailed info regarding Skippies! I have one, but for some reason never got back to this thread to post..... But you did a much better job than I could have!
Also, when I "flush" mine, I'll dump a few buckets of pond water over the media as the water level in the tank gets lower -- seems to help dislodge and knock down more debris that way.
And as to the bottom drain, I made a [I think....] 2" drain in the very bottom of mine with a shower drain thing or a closet flange.....whatever. The tank is elevated on cinder blocks to allow access to this plumbing since it comes out the bottom and not the side. I have a valve attached so I can open & close it easily -- that's how I drain the tank and do my water changes. The larger "hole" will move more gunk more easily. But
@lynntran since you plan to eventually switch systems, this might not be something you'd want to mess with right now. Not hard to do [there are instructions on here and all over the place], but does involve taking the filter down and moving stuff around during the process.
And while my Skippy does do a great job with bio-filtration, I haven't been happy with the mechanical aspect.