2/90x45 means what you thought . you can either nail them side by side, or bolt then either side of your stumps (with a notch in the stump for them to rest on.
you can use 90x90, but the program I have for spans, has 2/90x45 slightly stronger than 90x90.
If you have a look at the stickies at the top of teh "Decking" forum there is a great decking calculator, just plug in your dimensions and it works out what you need.
There are also several span tables. the last one is a very simple one I made up using F5 and common sizes.
What program did you download?