Will each of my second charge mortgage payments go towards the capital as well as the interest?
Your second charge mortgage is a capital and interest loan, therefore each monthly payment covers the monthly interest on the loan and a proportion towards reducing the loan itself. This means that each monthly payment reduces the capital amount that you owe (your loan balance). So your loan balance reduces over the term of the loan, and is repaid at the end of the loan term.
This assumes that you don’t miss any payments during the term of your loan.