On a real board or on chess.com? It makes a bit of a difference.
Chess Visualization

I find using the analysis board in my online games here on chess.com is making my overall visualization skills get worse, I suppose it's because I'm not practicing it as much as before.

Play blindfolded. For starters, only remove the queen, then the rooks, etc.
Don't forget to write down the moves so you can always go through them if you get lost.
This is the simplest and best method.
I have summarised some exercises to improve your chess visualisation here.
http://becomingachessmaster.com/2015/04/25/how-to-improve-your-chess-visualisation-skills/

Here is a kind of exercise I do from time to time. Tactics problems with the position shown being a few moves earlier than the tactical position. Then you look at the moves in between, visualize the end position and solve the tactic. You can create these problems in various ways, but there are a few books full of this type of problem, too. Also, I will be posting some of my own creation here, where you can already find five of them to try out:
http://www.chess.com/blog/pawpatrol/look-ahead-part-1
A couple of books that have this kind of problem are:
(trying to remember the titles, hope I've got them right):
Blindfold Essential Training
Checkmate Vision
Hell guys, what can you suggest me to improve my chess visualiton skills (seeing the whole board in my mind for example)? thank you for your supports