In this case, 5x5 means that one gridspace is equal to a 5 foot square in terms of game scale. So a token occupies a 5 foot square cube, if that makes sense?
As far as map scale is concerned, you will need to upload it to foundry and set your grid size to 100 pixels per tile (the default) and make sure that the map uploads at the correct size (6000 pixels by 5000 pixels)
Hope that helps!