What aspect is it you want to track? Invoices generated this way still have due dates which show up in the Notification panel if past due, and are displayed in the Invoice navigation panel, Invoice Management Window and Search scenes.

These invoices are showing up in the invoice management window in the 'Invoice ID management' panel, but they do not list the total, nor do they display project/client colour coding (as in the 'items awaiting invoice' panel). The invoice navigation panel is fine, but I like the modal box for the invoice management window as it allows me to display the invoice management window and the payment tracker window at the sametime.

Try using Invoices in the Search panel.  That shows totals and the Search panel can be kept open along with Payment Tracker.

Thanks for the tip — it's a little counter-intuitive to use 'search' for this — but it's helpful. It would be useful to see a column for 'Client" in addition to the invoice ID. I was surprised to see that the search index for payments is almost better than the 'payment tracker' window in that it lists payment method and cheque number. It would be nice if the 'payment tracker' window would list this data as well.

As described above, I wanted to use the invoice management modal box to view invoices created with an entered amount so that I could also have the payment tracker window open. I always generate invoices from an entered amount as I do not use automated invoicing or invoice directly from work items as me fee is negotiated at the outset of projects and paid in halves (half on signing, half on completion). I use work items to track my time and profit/loss (though they could be set-up better for this purpose as discussed elsewhere in this forum).