We really do need more information about your hitch etc.
I have the Reese round bar WDH with the dual cam system. I also had problems getting the chains perpendicular as you say. In my case, the tray that the propane tanks sit on was in the way of the brackets. I was able to unscrew the tray and move it far enough to allow for proper location of the chain brackets.
In doing some research on my problem, I found that Reese offers some alternative brackets that require less clearance on the frame. I did not like these because it seemed that they would make hitching and unhitching more difficult. But I never really inquired into how they worked exactly.
I recommend you call the help line for the hitch manufacturer. It's always better to talk to the experts than sift through all the information on the web. I spoke to the technical staff at Reese several times when installing my hitch. I found Reese to be extremely helpful and patient with me. I was able to correctly install my hitch and travel 18,000 mile across country without a single problem.
Forest River SP220 Sport
2013 Tundra 4.6L 4X4 Tow package