We recently built a shop and are now going to build a small extension pole barn type shed to store outdoor equipment to one side of the shop. What is the best way to connect the two buildings along the roof line? They will both be chicken-shed roofs.

Gable or shed roof? Drop the roofline 3-4" for clearance, lag a roof joist to the old structure, lag wall studs and build from there. Don't try to keep the same roof or wall line, it never looks good.