Well, shaking a sep-funnel is a great way of creating a horrible intractable emulsion with no clear phase boundary, so don't do that (also, the stopper might pop off as soon as you set it down).
As for breaking an emulsion, if you have the time, just leave the sep-funnel somewhere and wait a few days. I seem to recall the first and last time I shook a sep-funnel the lab tech added some salt to the water/diethyl ether emulsion however I'm not clear on this.
Finally, consider sacrificing part of your product by drawing the funnel off to the very base of where the emulsion begins, draining the emulsion layer entirely and then taking the remainder. If you have blobs of one phase in the other, you may be able to remove them with a pipette.