If your intercompany loan accounts are set up as bank accounts rather than G/L accounts, you can still use Balancer!
All you need to do is make sure the bank account is given an account code in Xero.
This can be added by heading to the chart of accounts, clicking the name of the bank account and adding in a unique code for the account
Once you have added the account code in Xero, be sure to re-sync your Mayday file using the sync button in the lefthand menu
You will then be able to set up the intercompany balance as normal. See this helpful article for more details.