"So
how do I pay myself back for those expenses"
Write Check and use your Employee name as payee. List what you Bought, that they are paying your for.
Example:
You bought Printer Paper. You write a company check to
yourself (the employee name) for Office Supplies and give the company
your receipt for Proof.
"Is it better to use the register of the loan account"
It isn't a Loan. It is reimbursement. If it was a Loan, you would not expect to be repaid in 2018 for expenses entered into 2017. The business did not Incur these in 2017. It isn't going to make your 2017 1120S.
"or enter the
expenses separately? If I enter them separately what would I use for the
Bank/Credit account or once I enter the loan will that show up there in
that drop down menu?"
First, stop thinking about Working in Registers. Use transactions: Banking menu > Write Check. List here what they owe you for, that you are submitting for Reimbursement under an Accountable Plan as an employee.
A Shareholder gives a loan, such as $50,000 deposit.
An Employee buys something for work, and the employer repays them, if the employer didn't offer the Money in advance, so that the employee did not have to use their own funds.