I'm not entirely sure I follow your reasoning: having "two Apple IDs logged in at once" doesn't solve the problem of purchases occurring in the context of an Apple ID - there is no way to purchase an app with two different IDs without both accounts being charged. (Please elaborate if I'm misunderstanding what you're asking :) )
However, across multiple devices, you can use a single Apple ID for purchasing, and separate Apple IDs for iCloud, if you want one source of purchases but separate sources of data / backups on each device.
The settings are distinct: In iOS, you pick the Apple ID used with the iTunes Store via Settings > Store and for iCloud via Settings > iCloud.
So, for example, you could both use your account for the Store, and have the purchases made on each of your devices.
That said, there is no easy way to use separate accounts with iCloud on one device, as setting the device to use Account #2 will blow away Account #1's data, making it difficult to truly share a single iOS device unless you don't care about separating your contacts, Photo Stream, etc.