Not sure how best to plumb in a canister. Check that link I sent you for ideas on where to run the lines. They figured out where to put them wthout having to do any cutting of the tank and so that the microbubble problem is fixed.
The problem I see with placing the line to the canister to the right of the skimmer (behind the overflow grate) is wouldn't the skimmer get in the way of the lines? You might be able to make it work with some cutting.
Regarding the original pumps, I'd leave both in. they are small pumps and having two gives a better mix to the flow. Also, if you remove the pump you need to plug the hole through the smoked glass
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