If you've received a loan, using the 'Paying In' category for that transaction will let the app know that this is an injection capital as opposed to income. For any repayments that you make on a loan, you should use the 'Loan Repayments' category.
Both the 'Paying In' and 'Loan Repayment' categories are not included in any self-assessment reports as income or expenses.
You won't be able to claim for the repayments, however, you can claim for interest paid on any business loans. You should class interest paid as 'Bank Interest'.