After you've connected your Shopify account to your Partial.ly account, you will see a Create Payment Plan option in the more actions dropdown while viewing draft orders in your Shopify admin.

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After clicking the create payment plan button, if the draft order has no customer associated with it you will be redirected to the create payment plan page where you will need to select or create a customer. If the draft order already has a customer, the payment plan will be created with that customer information.
If you already had Shopify and Partial.ly connected and get an error when trying to create a plan from a draft order, we might not have permission to create draft orders on your behalf. Try to disconnect Shopify from your Partial.ly merchant portal, then reconnect again.

After assigning the customer, you will create the payment schedule. You can enter your own custom terms for the plan, or use defaults by selecting the Apply from offer option then selecting one of your offers from the offers dropdown menu.

Potential issues to be aware of

Percentage based discounts combined with fees
If you set a percentage based discount on the Shopify draft order, then add a fee to the Partially payment plan, when the payment plan is opened and the Shopify order is created a custom product will be added to the Shopify order to represent the fee line item. This will cause Shopify to recalculate the discount, which would then include the fee line. Because of this, we recommend that you use fixed amount discounts on your draft orders if you will be adding a fee to your payment plans.

Taxes
Shopify will calculate and add taxes to your draft order based on your Shopify tax settings. If you then create a payment plan from the draft order and send the payment plan to your customer to complete checkout, if you have different tax settings configured in Partially the taxes will be recalculated according to your Partially settings, causing a potential mismatch between the payment plan and draft order tax amounts.