When we input the T5 which is joint and we are income splitting, do we each put in the full amount (which seems like we have double the investment money)

You will need to enter the full amount on both returns, but there is a box on the T5 where you can allocate a percentage of the income to your spouse. This will automatically calculate your income from the T5 based on the percentage entered so as to prevent double-taxing you and your spouse.