What do you mean by holes in the roof? Do you mean the rubber roof on top? How big are the holes? Dime, quarter, baseball, basket ball, round holes or rips? If it is parked permanent, you can build a roof over it. I wouldn't build on top of the trailer, but would plant post down the sides, and build above it. That way, if you ever had to get it out you could. Also don't know how much extra load the sidewalls will take.
Give us a few more details, and we'll try to help.
2012 Ford F250 ext. Cab 4x4
2002 Jeep Wrangler Sahara
2008 Yamaha V-Star 650 Classic
2008 Work and Play 18LT