I’m finding it very useful to assemble the dates and information that I have into a timeline. Then I can see what I have and where there are gaps. You can make one just on the Civil War years or include those with the complete timeline of your ancestor’s life.
For the time he was in the service, consult regimental histories to determine where the regiment was and what they were doing on different dates.
Here’s my example, a timeline for the life of Abraham Bates Tower.
I used Squidoo to create my timeline, but you can put it online with a blog or your own website. Be sure to back it up regularly in case anything happens to the site.