It might be that you may try adding the filler in smaller batches rather than all at once. As the viscosity builds up, the shear force that can be applied to clumps increases, reducing or eliminating the clumps. I've never had a clump problem. YMMV?
Whenever I've used fillers - with certain unique exceptions - I've used too high a filler mass percentage for adding epoxy to the fillers to work. The exceptions - making a slightly thickened initial coat for tacking down light fabric in a complex mold, and making a glass fiber blob of chopped cloth scrap for stuffing into corners of molds.
If you are having a problem with a particular filler, it could be that using another manufacturer's filler will work better for you, you might have a moisture problem, or it might be that a blend of fillers will work better for you.
Adding milled fiberglass first for instance will increase the viscosity during the mixing process, helping to pull apart clumps. IMHO it won't improve strength appreciably, but it may aid in the mixing process.
Most times I used a combination of fillers. 410 + milled fiberglass for lightweight peanutbutter filler, for instance. The volume of stuff which goes into the epoxy is way more than the initial volume of the epoxy. It's like the Donkey on one of the Shrek movies - Are we done yet?
If a filler is just to create a volume solid than it is ok to whip air into it (just don't make a dust cloud as that is uniformly BAD for you), so don't do the whipping until it is blended. But if a filler is to be structural, air is the enemy. So then you have to mix much more carefully, or possibly even consider degassing methods.
Fillers tend to increase the volume of the epoxy and to reduce its thermal conductivity. Epoxy is generally exothermic - some rather more so than others. Epoxy with fillers can cook itself off quite a bit faster than epoxy without fillers. Expect your working time to be reduced a lot, possibly by half even. You can reduce this of course by spreading the mix out in a thin layer on a plastic plate, a playing card, aluminum foil, etc, after or even during mixing depending on quantity required.
I've never done it, so I can't comment on it, but some people have mixed fillers with the component epoxy parts before mixing them together. That way at least you can mix for as long as necessary without concern for kicking off and killing your working time. But you have to be very careful of epoxy mass loss to mixing items messing up your ratio. It is probably better suited to larger quantities rather than small batches.
Epoxy with fillers can easily kick off hot enough to smoke, to melt plastic, or to burn you. You have to be careful once the batch size is no longer small.
Some less common fillers may be worth considering on occasion. Powdered aluminum in sufficient quantity makes a decent poor-man's tooling coat for a mold. It also increases the thermal conductivity so the center of the mix doesn't get quite as hot as fast, extending the working time a little compared to most other fillers.
Sorry, I typed much more than I had intended!
Gerald