There are two types of situations, depending on how invoices will be created.
(a) In the case of an agreement with manual invoicing, you can type the full amount in the agreement and, after the agreement is signed, when you create the invoice (BILLING > INVOICES > CREATE > Under Line Items "Bill for coaching" button > under Client Invoices locate the invoice draft and click the more option button and click on view), you can apply your 10% discount there.
(b) In the case of an agreement with automated invoicing, you need to type the discounted amount, because there is no way to apply a discount afterward. So, if the full amount is $1000, use $900 in the agreement and you can mention to the client that it's a discounted amount in the invoice note (that you can create for automated invoices in the Invoicing tab of the agreement wizard).
If you want to issue a single invoice for the full amount, check the "Pay in Full" option in the Coaching Agreement tab.
We suggest that you run a test before sending an actual agreement to a client, to make sure you set it up correctly.