There is nothing in the rules that prohibits or prevents PPP loan funds from being used for part-time as well as full-time employees. Pay is pay. The faster your eligible pay adds up the sooner you can apply for forgiveness. If you are going for the 8 weeks then you need ALL payroll as fast as it accrues.
You are, quite frankly, making more work for yourself as the Payroll Summary Report, along with filed 941 is what proves Gross Payroll. It is for EVERY employee except FFCRA paid leave, which is still payroll but the summary report separates those payroll items when set up according to plan
Some businesses, like restaurants and amusement parks d not have any full-time (or very few) employees and the PPP funds can certainly be used for a business whose ONLY employees are part-time.
Now as far as what you want to do now, if you feel strongly about separate tracking and DID NOT use a brand new bank account or existing slush account to hold funds and then merely transfer gross payroll amount after each payroll run as we did, is to make a QB bank transfer from your sub account to the master account. Banking>Transfer Funds