If you want an Allopathic residency...yes you are a slight disadvantage (I wrote about this in the Osteopathic Section), as many residencies will have a "limit" to DO's in their programs...just the way it works. But regarless of MD or DO, if you bust your butt, get good grades, score well on boards, and have an outstanding audition rotation...you make yourself a potential "first round draft pick" on match day. So do your best and everything will fall into place.
You will find that DO's have a larger voice in EMRA and ACEP than ever before.