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The only way papers won't change color is if they're on acid free paper. However, the polyurethane will help because it lowers the exposure to air and to a lesser extent light. Sunlight is probably the worst enemy. I believe there is a special formulation that is supposed to reduce UV rays.

As for a smooth surface, the only method I know works for sure is applying upwards or 5 or 6 layers and sanding inbetween each layer. However, if you are applying it over paper, I don't think you can sand. You might look into a pour-on resin finish like Envirotex.

Some polyurethane will yellow after time. Part of the charm on some things. Read the label about that.

For decoupage purposes, you may want to seal the 2D art with PVA glue or something so that there isn't any bleedthrough. For instance, cheap newsprint with a color ad on the back may show through. You have to experiment. There is no one way to do anything like this.

If the 2D item seals and dries with the PVA or mod podge and there is no transparency issue or bleeding of colors, then you can use it under the polyurethane. Just be sure it's cured first for at least 24 hours.

The polyurethane applications will depend on you to a great extent. If you are moderately skilled and finishing a flat horizontal surface in a dust free area, maybe three coats will be enough. If there is varying thickness of your decoupaged items, count on more coats. I like my last coat to follow at least one sanded coat.

Check the dry coat with a nylon stocking dragged over the surface. It will kinda snag on any imperfection that you then have to sand down with fine grit. Lightly buff the entire area to be covered with the final coat.

to solve bleedthrough problems, use color copies of the items rather than the originals.

My dad did this with his desk, but he just put everything on the table top and got a large piece of glass to cover it all. It doesn't shift around, and it gives a smooth surface to write on. I don't know if you can do that in this situation, but it's another idea.

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You could also use Lexan instead of glass - it's a clear, sturdy plastic and they sell it at the hardware store.

the glass my dad uses on my desk is at least 20 years old, and it hasn't cracked yet. it is a really thick piece, like what would be on a coffee table, and it's heavy so the pictures and clippings are weighted down pretty well.

if you don't move the desk much, and don't do anything really destructive to the glass, it should probably be fine. i just say this because my dad breaks things easily too, and it hasn't been a problem for him (yet).