Hi ashishw78
Taking from substrate will help a little.
I wouldnt advise using any water from an established tank. There is very little beneficial bacteria in the water column, so there is little to no benefit from doing this. All you will really getting are the bad things that might be living in there.
The best thing to move to your new would be a little filter media from the established tank, or get an old sponge and rinse it out into your water. You might still get something you don't want, but at least you know you are getting the beneficial stuff you do want.