Allergies or just a cold virus? Is there an easy way for the doctor to tell?

Not always. Allergies don't cause a fever, and usually last longer than a cold(>10days)..An itchy nose is more frequent with allergies, and the mucous from an allergy is usually clear...Severe aches = cold not an allergy..Check out this link http://www.Niaid.Nih.Gov/topics/allergicdiseases/documents/coldallergy.Pdf.
Not always. Both allergies and colds can give you runny nose, stuffy nose, cough, and sneezing. Allergies don't cause fevers, and colds generally don't give you itchy nose or eyes. If the inside lining of your nose is swollen and very pale, allergies are more likely. Also, there are blood tests and skin tests that can help diagnose allergies.