Tax year 2011 and 2012 - Tax time questions

[rsvpvr]

I received compensatory (travel , lodging expenses etc) allowance for over an year from my comapny. I need to pay taxes on the reimbursements I received. If I pay taxes based on w2 given to me by company, does that tax calculation by default takes care of my compensatory true up situation?
I took the help tax professional in submitting my tax return. But I did not inform him that I fall under "compensatory" situation and hence the above question.