IMHO it's best to get a second quote and compare, just print off another set of plans and use that for comparison purposes. Having someone come in and look over what you have the first guy doing will probably p*ss him off and will ultimately affect the outcome of your job.
Will you be here for the actual construction? Best investment you can make during the construction is a very comfortable lawn chair, park your butt in the middle of the site 8 hours a day and you will be amazed at the result.