How to properly use Income Accounts?

I’m also not sure why you’re trying to do this via journal entries rather than invoices/payments, but if you want to do it that way you certainly can. Journal Entries are 100% manual. If you want something recorded to an income account, you have to say so.

In this case, you’d need two more lines in a journal entry: $100 CR to an income account and $100 DR to a receivables account. If you don’t want to cancel and amend, you could create a second journal entry representing the other half of each transaction.