If I work in 3 states, I live in one of them. When I get to the percentages do I put the % from that state or the percentage of the total amount.$32,900 CT vs $20k in NJ?

Let's assume you live in CT and worked in NY and NJ.  Your W2 state wages boxes 16-20 will reflect CT taxing everything in box 1 and NY everything in box 1 and NJ only the NJ part of box 1.  Enter/verify the entries in TurboTax "Wages & Income" using the "Job(W2)" topic.

Work your non-resident states first.  In NJ you will be asked to "Remove" wages in lines that don't apply.  You will check the boxes for NY and CT leaving only the NJ wage amounts.  You will not need to allocate anymore since the NJ line on your W2 has already done the work.  At the end take note of the income taxed and the income tax for NJ.  Those numbers will be used to figure your credit for taxes paid to another state on your CT resident return.

Next, work NY non-resident.  In that interview since NY uses all the wages earned, you will need to allocate by whatever means you find reasonable in your situation.  It could be by number of days or by percentage of pay for example.  If you use the percentage method you could subtract the NJ income from the box 1 amount and then divide that by the NY box 16 amount to arrive at the percentage to put in the NY allocation box.  Continue the interview only allocating what belongs to NY.  At the end take note of the income taxed and the income tax for NY.  Those numbers will be used to figure your credit for taxes paid to another state on your CT resident return.

Now work your CT resident return.  Your resident state taxes all income from all sources, however, be sure to go through the credit for taxes paid to another state to verify/enter any necessary figures from the non-resident returns to mitigate the double taxation on income earned in the non-resident states.