I run my sumpless system with a DIY counter current wooden air diffuser skimmer and as mentioned, a Rena XP2 canister filter with a bag of carbon only. Actually I'm using an XP3 motor on the smaller XP2 container, ended up breaking too many mounting tabs on the XP3 container. I suppose the carbon bag itself acts as a bit of a mechanical filter in that it traps a certain amount of debris. It's nothing like a dedicated foam or poly pad though.
The only critter that occasionally messes with the sand bed (medium to deep in some areas) is my Maroon Clownfish female. Lately though, as my tank has matured, the sand bed is getting a bit of a 'crust' on it, preventing her from stirring it up at all. I stir it up manually from time to time to break the crust. Not sure why the crust is forming, I suspect it's because I've been keeping my calcium levels a little higher (above 400) with the occasional dosing. I use regular IO salt for water changes and that's known to be low, although the newer mix is supposedly higher.
FYI, I have two VorTech MP40Ws providing flow and although they're dialed down a bit, create quite an undertow and powerful movement throughout the system. If anything was going to stir up the sand, it would be them and that hasn't really happened, even when I had only one cranked up to 100%. Maybe that's why my tank is fairly clear, these pumps do not allow anything of a certain particle size to hang around in the system for very long. The VorTechs are about 3.25 inches from the surface at either end.
You don't mention how long your system has been running. I've found that as it matured, the sand bed became less likely to be stirred up. Seems to me I've read that most sand beds will do this, get 'heavier' with age and less prone to being kicked up, something about bacterial & critter colonization. Finally, I also ran a Remora C Pro with a Mag 3 pump and was not that pleased with it's performance, nor the excessive noise made by the injector nozzle. There are mods to deaden the noise, but I'm happy to be back to the old school, very quiet DIY skimmer. It does quite well and uses very little power. I have no problem changing the wooden air diffusers occasionally, compared to the power consumption and noise of the Remora. My skimmer uses a small AquaClear powerhead in a pre-skimmer box in the display to circulate the water. The pre-skimmer box also collects a fair amount of crud so if your Remora C does not have the pre-skimmer box that's available, that may be something to look at for improving performance and capturing additional debris. Drawback is that the box will take up a fair amount of real estate in your 29 gal.
EDIT: as an alternative to the pre-skimmer box, you could try one of these cheapo surface skimmer contraptions. Most LFS will stock these, takes a bit of fiddling and tuning and they'll still take some water from the lower intake. Much smaller footprint in the tank though. I hooked one to the Mag 3 and I'm pretty sure it helped:
http://www.jlaquatics.com/product/pf...e+Skimmer.html
So in the end, depending on the age of your system, depth of your sandbed and granule size, it may boil down to a matter of time to let it mature and perhaps some better flow to keep stuff suspended so your skimmer can remove it. Mechanical filtration may be a good option for the time being.