Unfortunately a bank account cannot be seen across multiple portfolios. In an ideal situation you would have a separate bank account for each portfolio, however, where that is not possible you can get around bank reconciliation by editing the bank statement that you are importing and only importing the transactions relating to their respective portfolios. For example:
You have one bank statement including transactions from portfolios A, B and C. Make a copy of the spreadsheet and remove all transactions relating to portfolios B and C. Import the spreadsheet to portfolio A. Make another copy of the main spreadsheet, remove all reference to portfolios A and C. Import into portfolio B, etc.
A bit long winded but it would allow you to manage the portfolios correctly as would certainly be better from a tax point of view to have three portfolios so that you can run the Income Tax report as per your ownership. You would need to run the tax report for the portfolio that you own and then again from the shared portfolio (entering your ownership value), export them both to excel and consolidate them.
All the best,