The best piece of advice is to talk to other students and faculty affiliated with the MD/PhD Program. The Program at Yale affords a great deal of flexibility and can be tailored to an individual's personal needs.
The reasons for pursuing a dual degree are as varied as the backgrounds of the students. There are 117 students enrolled in the Program as of September 2014, and they are seeking PhDs in departments ranging from the basic sciences to health care management. Living in New Haven and attending Yale can be quite an adjustment and it is very easy to feel lost. The faculty and students have made a concerted effort to assist you in whatever way possible both academically and personally. Please feel to speak with any faculty member, staff member or student about the Program.
The Program Handbook is designed to help answer questions specific to MD/PhD students. Items covered range from which classes to take for credit to finding a lab to re-entry. This is by no means an exhaustive info source, but hopefully will point you in the right direction when you do need help.