I am not sure where you are confused with Sharpcap.
You can use a guidescope to polar align rather than the main scope for a larger FOV. But there's no "mounting/dismounting" of scopes necessary.
The same guidescope used for PA can be used for star alignment (although frequently the alignment stars will be in the FOV of the main camera), and later on for guiding.
Actually I *do* dismount the guidescope, but that's because I have an OAG. I balance the scope without the guidescope, then put it on to use Sharpcap. Once I'm polar aligned, I take off the guidescope and go about my business (my mount doesn't require star alignment).