First - how can I just change to one of shopsite's basic buttons like the purple?
The Add to Cart and View Cart buttons for a Manager store are configured on Preferences > Store Text > Store pages. Other buttons for the shopping cart and other screens are configured on Preference > Store Text > Shopping cart / Checkout. Some themes will have actual buttons from images, but others will have text and then use one of the store color settings to put a colored background behind it.
Second- How can I customize all the buttons to ones I made? I think you can use a VAR change button?
See answer to the first question. Depending on the theme you are using buttons may be set on on of those screens. Some themes might use VARs to select a color, that would usually be done if the buttons are actually text and not images. When a VAR is used it may require certain colors to be set or the buttons go to some default color. You would need to view the template source to see if that is the case for your templates.
Third- how Can I set an on mouse over event class to a bulk amount of buttons? Is that possible?
This would require modifying the template and adding the on mouse over code. A web search for "mouse over event" should turnup some code you could use.
Fourth- I need some help restoring the custom thank you email and receipt pages. I had them set correctly at one time, but they deleted on the move.
The thank you email and receipt pages are in the shopping cart template which is selected on Commerce Setup > Order System > Layout settings.
Fifth - How can I add some subproducts to each more product info page? I guess I could manually edit the pages but is there a way to bulk edit this? Can you show me an example of how?
First, You shouldn't manually edit the ShopSite generated pages or your changes will be lost the next time you publish your store. If your products have subproducts make sure that the moreinfo section of the product template has a section to display them. It would need to have a [-- DEFINE SUBPRODUCT --] section and then where you want the subproducts to display section for [-- loop subproducts --] .
Sixth- How do i Resize the image size for the more product info page? I want to get rid of the scroll bar.
You can configure the size of the box the morinfo image displays in (if you have multiple moreinfo images) on Preferences > More Info pages. If you actually need to resize the images you do that on the Images screen. You configure the size you want the images to be on the Images > Configure screen and then on the main Images screen select the images you need to resize and click the Create Resized images button.