I have a pool motor, I have disconnected the double pole 20 amp switch and I did not mark them. I had to replace the motor, have 2 yellows and a green( ground). The switch has 2 loads and 2 lines, my question is, where do the loads and the lines go connected? Are the loads going down to the motor or should 1 line come from the Timer box( Line) and the other Load to the motor?

I'm not sure that I follow your post very well.

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I have disconnected the double pole 20 amp switch and I did not mark them.

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I assume that you mean a 20 double pole breaker in a disconnect box, some where in the vicinity or at least within sight of the pump motor.

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replace the motor, have 2 yellows and a green( ground)

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I assume that means you have successfully replace the motor.

A 240 volt circuit requires two hot conductors. Line or line side refers to the conductors bring power to that point. Load or load side refers to conductors taking power to the load (motor). Customarily line side conductors are attached to the buss side of the disconnect and load side conductors are connected to the breakers.

I don't understand the question about the timer. I guess it depends on the circumstance and intent of the original installer. Putting the timer on the line side would enable you to manually turn off the pump with out disrupting the timer. Putting the timer on the load side would enable you to turn off all power to pump including timer. That is most likely what you have.

Again I don't understand why this is a question for you. Just connect the line side conductors to the disconnect buss and the load conductors to the breakers.
Do you know which conductors are line and which are load?

You post does not say, but infers, that you think one load conductor goes to the pump and one goes to the timer. That of course is not correct.