One of the key features of eBird is the ability to map birds by precise location. Thus, each time you change locations or habitats it is best to start a new list. Locations can be as small as you want. In general, traveling lists should be less than 5 miles. Carry a notebook and keep track of these smaller birding locations, and remember to record birding time and distance!
Instead of trip lists, divide your birding into discrete units. You may even want to divide up larger birding areas into discrete areas as well. For instance, Malheur NWR with 50 miles between some locations should be broken into smaller birding units. Separate your birding lists into Headquarters, The Narrows, Buena Vista, Benson Pond, P Ranch, Page Springs, Frenchglen, Diamond, Round Barn, etc. Any unusual species seen while traveling between stops can be recorded as a "Casual Observation," located exactly where you saw them.
More information on this topic can be found on the eBird site, Location! Location! Location!.
Read all posts about eBird