No, they were two different films, as development for Road to El Dorado and Kingdom of the Sun (New Groove's original title) began in 1994 at both Disney and Dreamworks respectively. Although it's probable Jeffrey Katzenberg may have taken the basic 'Mayan' seed with him to Dreamworks, no serious development work had been done on Kingdom at that point. Kingdom of the Sun did have a very tortured production though, going from traditional Disney movie based on the Prince and the Pauper (complete with full-length Sting soundtrack) to an anarchic 4th wall breaking comedy (complete with a Sting song over the end credits).
The whole madness of the production is captured brilliantly in The Sweatbox, a documentary Trudie Styler made at the time, which was subsequently banned by Disney, as it showed the company in a bad light (understandably perhaps considering it was the doc director's husband Sting that was being messed around by Disney).
Fortunately, a copy slipped onto the internet a few years ago, and thanks to YouTube though you can watch it here, right now: