You must apply using the EIN for the entity that received the First Draw PPP loan. You must aggregate your calculations for your separate locations that are eligible for RRF. You may not include gross receipts (or eligible expenses, if using Table 3 from the application) from locations that are not eligible for RRF.
However, there is an exception: If your locations file taxes under a parent company's tax returns, you must apply under the parent company's tax identification number, and you must include gross receipts and/or PPP loans from eligible entity types/locations (for example, restaurants). You must also include PPP loans (but not gross revenues) received by any business that reports revenue through the parent company, regardless of business type.