Which way to invoice is better?

Hi there - Sorry I am just starting in business, and learning. Questions now, less headache later.

I will have to invoice customers like this:

1. Give them an estimate of total cost of a commission based on various options.
2. When they approve the estimate, their First payment is 50% of the total cost (not including shipping/insurance/tax). Second payment later on to be invoiced is 25%, last payment of 25% + shipping/tax/insurance.

I am trying really hard to figure out a way of setting up an Estimate, and then invoice.

Question 1: Should I invoice them with one invoice, that somehow can be paid at dates to be determined, in the three increments I mentioned above?
Or should I invoice them three separate times? I ask because it seems like having to send three different invoices based on one estimate might really get confusing within the Zoho system.

Question 2: Also, I can't seem to find any way to add shipping or insurance after the sub-total. Shipping will need to be a manual item, insurance would need to be 4% of the actual cost of the item.

Help really appreciated!!! Thank you..

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