First time with new boat and not sure if the air conditioner is even working correctly. There was a T fitting down by the water pick up as well as a small clear strainer. Hooked an antifreeze source to the t-fitting. I got the fan to run on the air conditioner, but the pump that would draw from the pick up never ran. Therefore I know fluid never went uphill to the air conditioner, but did go backward through the pump out the bottom of the boat.

What is the correct way to get anti freeze in the system or ensure that it is completely clear of water?

I have a diff set up but similar in a way. I shut off the sea cock and open the top of the strainer. I then turn on a/c or heat and pour antifreeze directly into the top off the strainer untill my buddy see's pure pink antifreeze coming out the side the boat. shut off a/c and done. If your pump isn't working than you need to get a new pump.

If the pump isn't working or it's too cold in the boat to get the AC cycle to turn the pump on, disconnect the pump and either gravity feed the antifreeze thru the system or use a pump and pump it thru till you see pink coming out the side of the boat. Be sure to fill up the strainer with antifreeze as well..