Should I apply % of joint investment income before entrering the amounts? or the system takes care once I identified my % vesus spouse's %

You can enter your percentage amounts for your joint investment accounts at any time while on the T3 or T5 screen in TurboTax. As soon as you click "Done with TX" your entry will be saved.

You only need to enter the T-slips on "one" spouse's tax return and specify the % split. If you enter them on both returns, it will result in each of you claiming twice the amount. 

Incomplete answer. It should also mention that T3and T5 data should be entered only once and not on both taxpayers.