Like Jon said, the conundrum is real... Getting an organic sounding acoustic tone through an electric amp is tough. So, in that, it depends on what your expectations are of your electric guitar and acoustic guitar tones independently of each other.

I would scratch the idea of micing an acoustic into an electic guitar amp to start with. I would look at a soundhole pickup like the LR Baggs M-1 pickup. Can grab one for 100 bucks on MusiciansFriend.com... This will get your acoustic signal into an amp friendly signal path while still giving a good representation of your guitars tone.

The trick with going back and forth between an acoustic and an electric is controlling the volume levels between the two. The input levels are going to be drastically different so one channel won't suffice for both instruments. You would want something with either two channels or two inputs and independent volume controls for each channel/input. This will allow you to simply switch between the two by selecting a difference channel or input and the volume levels will remain in check.... This will also help control feedback.

As for an amp... a Vox AC15 comes to mind. It has a great capacity for clean tone but can get really dirty in the Top Boost input. You could run your acoustic through the Normal input and your electric through the Top Boost input and simply use an ABY pedal to select which input is active. Each input has a designated volume and the amp has a master volume.

Hope that gives you some ideas.