You can create an invoice from the Tenant's Lease tab, and Current tab. Either on the Properties page or the Accounting page.
Click New Transaction to create a new invoice. This is a blue button on the right side of the page.
This will open up a small section here to enter the details of the invoice. You can set an invoice number, choose the Item of the charge, choose a site (defaults to the tenant's unit), add a description of the charge, choose a Company (defaults to the Company owning the tenant's unit), and the amount.
If you do not see an item type listed that you would like, select Manage all the way at the bottom of the item dropdown and you can add more custom items (and associate them with specific accounts). Then scroll down in this Manage Items lightbox to add New.
If you want to charge the tenants for multiple different things (for example rent and parking), then click the three dot menu on the right side of the invoice, and Add Line Item.
Be sure to click Save in the bottomright when you are done with an invoice.
You can also create invoices from the Tenant's Transactions tab under Accounting. By clicking New on the top right and choosing Invoice.