I have to say, that my common-sense approach would have been than if you have a Direct Debit set up, then anything that you would pay manually would be charged in addition to your DD arrangement. I'd think that you'd have to effectively cancel the DD every time you wanted to pay manually, and then set it up again (which is obviously a non-starter). If other providers managed to hold back on getting the money from DD after you had paid manually, I wouldn't have thought that this was proper practice. I'm going over the DD guarantee document now and I can't find any reference to being able to vary your payment methods, or indeed what happens when you do so.
I pay manually every month, in full, for three cards. Considering how easy it has become (just put your debit card's CCV) it's a two-click affair that makes sure that no matter how high or low the amount is, I get to check before I pay. I'd be interested in finding out what's the proper practice in flipping between manual and DD though...