I really reallly hope you mean hooking it up with prefilters attached. Do not ever hook it up without prefilters attached because you will ruin your membrane, there is no if's or but's, it's will get damaged, a lot.

You never check pressure on the flush setting, because it will be incredibly low. Do not close the flush valve completely.
To do this properly, to make a 'flush kit', you need two 'Y' pieces, four pieces of garden hose, and two inline ball taps, and a load of jubilee clips. This is all 1/2" btw. Connect the first 'Y' piece to the waste pipe. Fit the two hose pieces on both outlets. Put one valve on each hose piece, then put the other two hose pieces on both valves. Connect the two pipes coming out of the valves to the other 'Y' piece, and connect the 'Y' piece to the rest of the waste pipe.
This way, you can have one valve set to a preset standard so you have a 60/40 or 70/30 waste to pure ration. The other valve you simply open all the way if you want to flush the 4040.
To measure the correct ratio of pure to waste, get a stopwatch, measure the amount of pure produced, and the amount of waste produced. So let's say after 1 minute you had 1500ml of pure, and 3000ml of waste. Add the two together, which is 4500ml. That is 100%, divide this by 100. Which is 45. To get the percentage of pure and waste, divide the 1500 and 3000 in this example by 45.
1500ml pure = 33.3%
3000ml waste = 66.6%
So your ratio pure to waste is 33.3/66.6, a safe figure.
Hope that makes any sense to you.

Edit : Picture attached, sorry for the low quality. I made this real quick when I first setup my 4040, it looks a bit more decent now with clear, reinforced tubing and is cabletied to the tank cage.