Ask Mr. Smarty Plants

As you have already discovered, I'm sure, the differences are not obvious.  In fact, they are VERY subtle.  Erigeron strigosus (Prairie fleabane) was once considered a subspecies of Erigeron annuus (Daisy fleabane).  (Erigeron annuus ssp. strigosus is the synonym for the accepted name Erigeron strigosus var. strigosus.  See the entry from ITIS–Integrated Taxonomic Information System.)

You can read a description of E. strigosus and a description of E. annuus from eFlora.org, the online version of Flora of North America.  There are many technical botanical terms used in the description.  If you have James Harris' excellent book, Plant Identification Terminology, you shouldn't have any problem working your way through the terms.  If you don't have Harris' book, here are a few sites that should help you.  For leaf shape, try the Berkeley Echo Lake Camp Leaf Shape Terms and Leaf Shapes and Arrangements from The Seed Site.  You can find a very good list of Botanical Terms on the Calflora.net site.  Reading through and comparing the descriptions, you can see there are small differences in the types of hairs on the stems and leaves, the leaf shapes and whether the leaves persist during flowering.  You will also note there is considerable overlap in sizes and numbers of structures.  E. annuus is listed as having 5–50+ flower heads and E. strigosus is shown as having 10–200+, but still there is some overlap.  Just to complicate things more, please note the statement at the end of the description of E. annuus:

"Apparent intermediates between E. annuus and E. strigosus are encountered."

If you go to the 'parent' page for Genus Erigeron on eFloras, you will see that the the genus is divided into 23 Groups.  E. annuus and E. strigosus are part of Group 4.   The key to Group 4 of Erigeron spp. summarizes the differences in the two species and is a bit easier to get through; but, as you will see, there is still overlap in the descriptions and you are going to need a magnifying glass to see some of the differences.

Good luck in distinguishing between the two!