Dennis Sellers at the Rocket Yard at OWC’s Blog has the best way to fix this issue. I did it years ago, honestly having 2 menu bars and docks is just confusing to me, but I have been using a mac with 2 monitors for a whole lot of years.
A great article on why you should use OS X spaces. I love it personally, though I think you had more control with older versions. And it is especially great for laptops, but I use it to separate power apps on my macpro and couldn’t function without it at this point.
It is now part of Mission Control (though should be it’s own thing). It makes your mac have a virtually bigger space, as if you have a bigger desktop and are only seeing part of it and can set individual apps to different spaces.