I use an MPC for my breaks, personally, so I don't have any comments specific to EOS samplers...
But anyway, I like to EQ 'em before layering. Usually strip off the low end for all but one of them (let that one dominate the low end). That also lets you layer without worrying as much about clashing kicks or slightly off timings. Sometimes other EQing helps as well. All in all, it's somewhat of a bitch
What I would like to do is try using the Emu and loading up several breaks with an LFO controlling amp volume so that they fade in and out of each other. That could create a very nice effect...