When I set up my new Freesat box today, I was slightly disappointed to see that the SD quality of the channels did not improve that much compared to my old Sky box. Is there a way that I can set the upscaling on (or off to let the TV upscale). I also wanted to ask if the twin tuner satellite cables had to be entered in any specific way because I randomly plugged them both in.

Both LNB feeds are identical, so it makes no difference.

I don't see why you expected a Freesat box to upscale better than a Sky box?, all upscaling does is make it fill the screen - it doesn't 'magically' create HD from an SD source.

Up scaling (if necessary) is controlled by the output resolution you choose (I think you get 1080i by default).
1080p looks very good on my TV especially on HD channels

Any upscalling of SD content is going to be dependant on what and how source material is broadcast.
If it's poor quality to begin with or they broadcast at a rather compressed rate then no amount of upscalling will make it look any better, it's only going to help to not make it look any worse on a large screen.

There is more than one algorithm available for upscaling so it's perfectly possible that one box could upscale better than another.

Of course it's go b all to do with whether the boxes happen to be Freesat of Sky.