So in a possibly misguided refusal to just give up, I digested this lengthy thread from the Avid forum -
http://duc.avid.com/archive/index.php/t-289728.html
The overall conclusion seems to be that, yes, you do need an external word clock to get multiple devices to be EXACTLY in sync with no jitter at all.
Obviously this is impossible for those with low-end gear that doesn't have that functionality, like me. Now that I've got a bit of an understanding of what clock and jitter and resampling actually mean I'd experiment with every combination of settings and thought I might as well post here in case other people have the same problem.
From reading the Avid post, it seems like you're supposed to set one interface as Clock Source/Master and then have 'Resampling' selected for the other device, so that in theory that device will resample to the sample rate of the master device.
I tried it set like that (One as Clock Source/Master, Emu as slave with Resampling selected). It started off working fine but after about 4 minutes of recording the jitter was very noticeable on the Emu tracks.
So I changed the settings so that the One is also set to Resample, thinking 'surely this can't make a difference'. Well... (touch wood) I'm now at about 30 minutes of recording with no jitter.
I'm fairly sure that this isn't going to turn out to be rock solid and either the jitter will start soon, or next time I use it it'll jitter after a few minutes. Fact is though, when I record on three inputs at once a 'session' only tends to be 3 or 4 hours, so if I can get that far without it descending into explosions of aural horror then I'll be happy.
Bottom line - if your aggregate device is causing jitter, try every possible combination of master/slave and resampling, as there might just be one that is at least usable.