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1. How do we count for the Rank tracker checking and creating visits to our site when IP is always changing?

Not sure I get you here. Rank Tracker does not visit your pages, it only loads the SERPs and searches for your URL there, but it does not load your page.
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2. When checking rankings for a company does it matter if it is a page inside the domain ie: shoes.com i optimize for "blue shoes" and shoes.com/bigshoes/womens/876/shoe and im optimizing for "red shoes"

If you start your project for your domain, all the pages located on it will be picked up, the highest ranking page for each keyword. So if your shoes.com/redshoes/ page ranks highest for "red shoes", it will be listed as "URL found" in Rank Tracker.
If, on the other hand, you start your project for shoes.com/redshoes/ then your homepage will never be picked up or tracked.
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3. does the location matter on our google?ie: it says your location is st. charles

Yes, it matters for some searches. In Rank Tracker there is an option to set your geolocation, which is similar to that.