This is a great question. I know it's important to have a grasp on the services your using and how they work. I can help you with your payroll remittances in QuickBooks Desktop.
I'm interpreting your question in a couple of ways. The first way is that you're asking how to manage 2 CRA payroll accounts in one company file through QuickBooks Desktop. QuickBooks Desktop's payroll subscription is great for keeping track of your company's payroll, including remittances. With a payroll subscription, you're able to track one CRA payroll account per company file.
The second way I interpret your question is that you have two company files, each with their own payroll and you're wondering how to handle your payroll remittances. In this case, I have a great article that can help you out managing payroll remittances: Pay or adjust payroll liabilities
If you have more questions about this or would like a hand with the steps outlined in the article I've included, don't be afraid to reach out to support. Dial 1-877-772-9158. Check out the following page to learn more about support hours and policies: Intuit QuickBooks Desktop software support policies
Enjoy the rest of your day!
This is what I do in this situation.
The first thing I do is create a custom field under 'Additional Info' on one employee's payroll profile. When you create a custom field in one person's record, it is available in everyone's record. I would call it something like 'CRA P/R Reporting' or something similar. I then open each person's 'Edit Employee' window, go to 'Additional Info' and populate the new custom field with either RP0001 or RP0002 (I'm assuming those are the two payroll accounts you have to report on). Pull an employee details report, choosing that custom item to display on the report. This will simply help you identify which people belong to which account.
At the time of filing for payroll remittances, bring up your PD7A summary. For each $ figure, drill down to open up a report with all the transactions. For example, double-click on Gross Payroll for period. Now set a custom filter and choose multiple names, and go through your employee list, selecting only those who are RP0001. Rename the report something like Gross Earnings - RP0001 and memorize the report.
Then double-click on the Total CPP Contributions, set the custom filter to choose only those employees who are RP0001. Rename the report something like CPP Contributions - RP0001.
Do the same thing for Total EI Premiums.
Then repeat the whole process, choosing only the RP0002 employees, renaming and customizing the reports.
Now you have two sets of reports, giving you the amounts you will need to report for each CRA payroll account. It sounds like a lot to do, but is very slick once it's all set up. Just ensure that the totals of your RP0001 and RP0002 reports match up to the overall total of the PD7A Summary.
If a new employee is hired, then you will have to go into the name filter and choose their name for the appropriate RP0001 or RP0002 report and re-memorize and replace the report to include the new employee(s).
I also went so far as to create a spreadsheet each month by exporting the PD7A Summary to Excel, then adding two more columns. I enter the amounts from my reports for RP0001 and let the spreadsheet calculate the difference for RP0002, which is another check and balance that your two amounts equal the total. This is not a necessary step, but I like to do it so I have a PD7A visual of the amounts reported for each account. I would give you an example but the community will not accept my excel graphic as valid posting material, not sure why.
Then go to Payroll Liabilities-->Pay Payroll Liabilities. Click on your Payroll Group (CPP-Company, CPP-Employee, etc.). Edit the Amt to Pay to the RP0001 amount. Create the payment. Enter RP0001 in the memo line after your Business number. Then repeat this process . . . what should be left in your Pay Liabilities window for the remittance amounts are the exact amounts for RP0002. Create the 2nd payment and identify RP0002 in the memo line. Now make your payments electronically, or however you do them. Make sure however you make your payment that you have identified the payment to the correct RP account.
Again, a rather inelegant solution, but it's the only way I've found that works.
1. When doing your T4's for RP0001, select only your employees who are eligible for an RP0001.
2. Prepare the T4's and file them as you normally would.
1. Go to your Company Information window in the Company menu. Change the Payroll Identification # to RP0002.
2. Go to your T4 filing and select only your employees who are eligible for an RP0002 T4.
3. Prepare the T4's and file them as you normally would.
There are situations where you might need to create a T4 of RP0001 and RP0002 for the same employee. This happens if something about your legal entity changes partway through the year. In this case you have to create two different employees, with something amended in their name, such as John Doe - 01 and John Doe - 02. Just make sure in the payroll record field Print Name As you take the number off. This ensures the name prints correctly on all forms.
The field on the T4 forms that contain the business payroll identification number is pulling from the Company Information screen. This is why you have to run each group separately and change the number from one to the other. Upon completion of T4's you can change it back to RP0001 if you like. When completing payroll remittances each period, I manually override the RP # in the memo field of the payment for the RP0002, as I have company information set to RP0001 as a default.
Hope this helps.