It sounds like you are literally and figuratively in a mess. It is not easy to work with an owner who has given a whole new meaning to the concept of leaving a paper trail.
If you are truly inclined to help the owner without confusing or upsetting him, the first step is for the two of you to meet. Although it may be tempting to simply go out, sort out, clean out, or throw out, doing so unilaterally may cause real problems.
There can be any number of reasons for his messy management style. For example, he may actually enjoy an office that looks like a ticker-tape parade on the morning after, or perhaps he still enjoys leaving his toys around and having others pick up after him. When you meet with him, let him know about the problems that the wall-to-wall paper is causing, and tell him that you would like to help gather and organize it. Then ask him how he would like you to proceed.
In terms of the bigger picture, it will be helpful to review whether the paperwork that is all over the place is needed in the first place.
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