Yes you can - my Ipad2 is the 3G+GPS version.
It appears that the operating system's GPS API automatically uses an external GPS if one is found.
Quite how it decides whether the external one is more or less usable / accurate than the internal one, I don't know.
It's the same issue with auto selecting WIFI v. GPRS/3G for internet access, and on those the Iphone/Ipad products do it poorly, if both sources are roughly equally poor. In fact they tend to lock onto "unsecured" WIFI access points but most of those are nowadays commercial pay ones which provide no connectivity, so if you want to use GPRS/3G reliably you want to switch off WIFI. But there is no config option for selecting the GPS source similarly.
I don't know if any Ipad apps have an explicit selection for the GPS source. MM certainly doesn't.
I don't like the idea of an external GPS, due to yet another thing which needs to be charged up etc. In my plane I have an old bluetooth GPS which has an external antenna socket and an external power socket, and it is velcroed under the dash and wired to a dedicated rooftop antenna and is powered from the aircraft. Any moving map device can use it. But of couse no Church of Jobs device will talk to a standard NMEA GPS
I am not aware of any Ipad compatible GPS (there are I believe just 3 or so types, against the hundreds of NMEA ones) which can be thus connected. So I don't use the Ipad for navigation when flying.