The doubling will be caused by you simultaneously live monitoring from the POD and software monitoring in your DAW. You need to turn off the monitoring in the DAW, that way you can monitor your playing from the POD in real time, without the latency delay caused by DAWs.
'Same' is only an option on 'input 2'. It just means that it feeds the same input as input 1 into input 2. So, for example, if you change input 1 from 'guitar' to 'mic', input 2 will automatically change as well. In the customtone Silverhead posted, input 1 is guitar and input 2 is mic (as far as I know), so you have two separate signal paths for your two different inputs.
'Global' and 'preset' are options to update either all or one patches from the settings menu. So for example, if you set input 1 as guitar, input 2 as same and set to global, it would update all of your patches with those settings. If you use a wider range of settings (such as a mix of guitar and mic), you would normally be setting these options for individual patches.
The input impedance option is a bit of a mystery to me. I don't really see it making a huge amount of different to anything, so I leave it on Auto. Someone else here will be able to explain it better, no doubt.
And finally, yes, you should be able to do everything in Edit that you can do on the POD, and vice versa. It's all very different, though, so it takes a bit of getting used to.