Timing

In trying to create my music I really have trouble figuring out the timing. I am using my piano sheet music and hymnal. When I create the music here it sounds okay. When published it seems so choppy. What am I doing incorrectly. Music was set to 3/4 timing per measure. I notice that the measures on the creation staff are different colors for 3/4 time there are six positions to place notes. Assuming there are two note positions per note count. Is this an incorrect assumption? Practice, practice, practice. Eventually I'll get it. Have a great day.