Do I have to keep all the magazines or books I find in my inventory to get the perks they give .seem to clutter things up a lot.

No, you don't need to keep them in your inventory. You can confirm that the bonuses exist by checking the Perks in your Pip-Boy.

So freely build furniture where they are supposed to be stored and display your collection.

Thanks , I didn't want to lose em by putting them somewhere without knowing

Magazine racks at home base are a good place for them.