My American passport says that I entered Amsterdam and that I left from Germany over a month later... once I returned directly to Germany. I proceeded to stay longer then the 90 day period. But my passport only has me as being in Germany for about 59 days of the 90 because I was stamped in Amsterdam before continuing the Germany. Am I still ok to apply for a Schengen visa so that I can return to Germany for another trip?
No, you can't do that. As I wrote in the comments, it doesn't matter if you were in Germany, Holland or somewhere else in the Schengen area. US citizens cannot get a schengen visa, but they are allowed to stay 90 days within a six months period.
As I understand you were 2 times in the Schengen area: once for "over a month" and later for 59 days. So you were around 90 days in the Schengen area and have to wait before you are allowed to enter the area again. For more information see About Schengen 90/180 rule.