There are several potential methods for charging your agency fee. You can either deduct it from the educator's pay, or calculate the difference between the childcare fee and the educator's fee.
Method 1: Deduct from Educator Pay

Note: If you're using this option, it's recommended that you disable the option to "Use educator fees to calculate educator earnings" on the Dayhome tab of your Settings page. Disabling this option will remove the educator fee fields from the dayhome educator's page, as well as the child's Fees & Discounts page. If you do not disable this option, then you will have to set the educator fees to match the childcare fees. Disabling this option will remove that requirement and simplify your billing.
Before you deduct the agency fee from the educator's pay, you must first ensure that the fee is included in the educator's pay. There are two different ways to do that. You can either include the agency fee in the childcare fee, or list it separately on the invoice.
Option 1: Include Agency Fee in Childcare Fee
If you want to include it in the childcare fee, then simply increase the childcare fee by the agency fee amount. For example, if the childcare fee is $900, but your agency fee is $150, then set the childcare fee to $1050. This way only a single line item will be shown on the invoice that the parent receives, and the agency fee is invisible to the parent.
Option 2: List Agency Fee Separately on Invoice
Alternatively, if you want the agency fee to be listed separately on the parent's invoice, then leave the childcare fee at $900 and add an "Other Fee" to the child's Fees & Discounts page. This "other fees" feature can be used for any number of additions to an invoice, such as a a lunch fee, transportation fee, or admin fee in daycare settings, or, in the case of dayhome agencies, your agency fee. To create other fees go to Admin > Finance > Other Fees. Once you've created your fee there, you'll be able to use it on each child's fee page.
On the child's fees page, scroll down to the Other Fees section, and add a new fee here.
Deduct Agency Fee from Educator Pay
Once you've got the agency fee included in the educator's pay, you can deduct it using a deduction payroll item. If you haven't already done so, create a deduction in Admin > Finance > Payroll Items. Create a new Payroll Item of type Deduction, name it "Agency Fee" and set the amount. This deduction will then be automatically listed on each dayhome's Enter Earnings Calculator.
Method 2: Calculate the Difference
With this option, the agency fee will be calculated as the difference
between the childcare fee and the educator fee. The childcare fee is what the
parents pay, and the educator fee is what the educator earns.

Note: For this method you must have enabled the option to "Use educator fees to calculate educator earnings" on the Dayhome tab of your Settings page.
There are two ways to set the educator fee. You can either set the child and educator fee on the
dayhome profile, or you can set both on the child’s fee page. If all
children at a dayhome pay the same fee, then it makes sense to set it on the
dayhome profile, but if each child can have a different fee, then it makes
sense to set it on the child’s fee page. In most cases, it's recommended that you set the fees on the child's Fees & Discounts page, and ignore the fees on the dayhome Fees page.
If you’re setting
it on the dayhome profile, go to the Fees page on the dayhome.
(The Fees page can be found in the dayhome menu) So for example, if the
parents pay $900 and your agency fee is $100, then set the educator fee to
$800.
If you’re setting
it on the child’s Fees & Discounts page, then set the child fee right at the top of the
page, and use a custom fee.
To set the Educator
fee, just scroll down the page a bit (on the child’s fee page) and select "Pay Custom Educator Fee", and enter in the fee the educator earns. (if you select “Pay Primary Educator Fee” here then
it will use whichever fee you had set on the educator’s fee page). Note: This “Educator Fees” section will only be visible if the
child is assigned to a dayhome.

With this method, and the option to "Use educator fees to calculate educator earnings" enabled (on the Dayhome tab of your Settings page), the educator fees, rather than the childcare fees, will be automatically populated for each child, on the educator's Enter Earnings page.