One thing to remember as you read Joshua 10:36-39 (and back in Deuteronomy) is that some of these stories likely include the use of hyperbole.  Phrases such as “thou shalt save alive nothing that breatheth” (Deuteronomy 20:16) and “utterly destroyed all the souls therein” (Joshua 10:39) sound like God gave the Israelites permission to start a genocide.  

But if you fast forward to Joshua 15 you’ll find that these same cities that the Israelites supposedly destroyed still had Canaanites living there.  So it seems that Joshua– like other authors of his time who wrote about battles– used hyperbole (​​exaggerated statements or claims not meant to be taken literally) rather than speaking literally.  (For more on the use of hyperbole in the scriptures check out this article from Meridian Magazine and episode 593 – an interview with Professor Trevan Hatch– of the One Minute Scripture Study podcast.)