I have an ECU connector that has 2x24 legs, but in plan the small leg is hidden under the larger leg.
In breadboard view can I draw 1 leg, but put 2 contacts on it and label them separately?
PDF dwg
http://www.te.com/usa-en/product-174917-6.html#pdp-optional-registration
Got to love ECU headers 
You should be able to manipulate things in such a manner. 2 connections at one point with 2 different labels? Look in the ‘core’ parts bin and mess with the labels, maybe that will work for you?
When assigning contacts in BB view I select one of the legs - as an example the LED - and assign one contact as South, select it again and assign the 2nd contact at Centre.
very good. thank you