"My question is, if I choose PayFlow Link does that include only credit card purchases? If we want to also allow them to log into their PayPal account, is that why I would check the box for "Include the option to with PayPal Express"?"
YEs, clicking the option to include paypal express would give both checkout methods.
"Also, is there a simple way to convert this from express to PayFlow link?"
The simplest way to convert is to delete the existing checkout pages and re create them using the checkout wizard.