Hi Miguel!

There are not any restrictions to switch-on several files from different stages in the same time. Except how many files can be opened in one time.
You create whole model, separated by stages, and can look on it as you would like.

Concerning stairs and similar.
First of all, and this way is the way by default, you have to place stairs in their own files, and switch the file with 1st-stage's stair together with a file with a plan of 2nd-stage. The same is true for slabs and others from under stages. In the result, you will see 2nd-Floor plan with 1st-Floor stair.
You could also use layers.
Third way - you can use associative views and show there which elements you want to see.
Of course, you can use any combination of all these three ways.

But for your case the first way is quite enough. Second and third - for some special cases.

In some cases, when you can't use these ways and really have to draw lines, you can to simplify it - just make a hidden/wired lines calculation from selected element - and you will have a base for this drawing. It is not needed to draw lines for any existing element from the bottom. And if you suppose to use it in the future - save it as a symbol or macro, to process the next drawings faster.

Concerning changes in the model and additonal graphics.
There are two main tips:
- If you decided to use any additional graphics, then keep in memory there you placed it. Or make a note in the file name. This way is very similar to users of traditional cad.
- Place additional graphics on the final stage of work, when changes will not come anymore. Of course, there can be some such "final stages" , so keep in mind a tip no.1.

Regards,
Alexey