Of course, Spanish is spoken in many different places, so it's natural that there are lots of variations (in the same way that the English spoken in England is different from the English spoken in New York).
However, they're not as different as many people think. I have no problems understanding someone from Latin America (we can guess the meaning of the words that are different, and the accent is not a barrier). Many of my students are more familiar with Latin American English, and yet they can perfectly understand me.
There is no such thing as "neutral accent" in Spanish, as David has said (and if it existed, it would probably be either Colombian accent or Castilian Spanish accent).
My suggestion: listen to the different accents and, at the time of speaking, stick to the one that you like the most, but try to get accustomed to all the variations so that you can understand Spanish in its may different forms.