I actually clear them both, no problems for me. But as I mentioned in a previous post, you do have to make sure your FCM's Risk Manager is on board and can enable your execution platform to recognize the overnight SPAN margin credit offsets on an intraday basis. It is also somewhat sensitive to the front-end you are using - I know for a fact that Pats is terrible to work with from an intraday spread margining standpoint. TT and CTS appear to be rather simple to set for it.
If you let Terry Duffy over at Advantage know what you are doing, he will make sure that Risk makes the required adjustments to your account settings. Both Man and Advantage (and RCG, RJ O'Brien, Cunningham, etc. etc.) clear many large spread traders - individuals, prop, institutions.
The big piece is that the margin offsets are not automatic on an intraday basis - you have to make sure that your FCM has made the correct allowances. I have also seen it where the FCM does not give you enough of a margin offset allowance. For more retail-oriented FCMs it is a huge issue, because all of their clients are trading futures flat price directionally with outright risk and they typically don't want to be bothered.