Introduction

Joshua divides Joseph's lot for both the tribe of sons (Ephraim and the other half of Manasseh). Though Manasseh was the eldest, Ephraim's portion is given first. Manasseh still receives the largest portion of the two and possibly overall (only Judah's territory appears to be larger).
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The Tribe of Ephraim

Ephraim is given territory to the northwest of the Dead Sea. The territory Ephraim receives is much smaller than that of Manasseh. The only water source they seem to have in their borders is the Yarkon River. "The sea" is mentioned in Joshua 16:6, so depending on the location of Michmethah, perhaps there is a coastal city. Like Judah, there is a city in the territory the men of Ephraim didn't fully conquer: Gezer. The people of Gezer are not driven out or killed, but instead are forced to served as tribute to Israel. Scholars suggest that the Israelites spared the inhabitants not out of mercy, but out of covetousness and greed.^[1][2]
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The Tribe of Manasseh

Manasseh received a huge portion of the land, especially when you include the land east of the Jordan. Manasseh's son Machir is described as a man of war; he must have been a leader in the battles against Gilead and Bashon. Likely, this is why he received the land east of the Jordan. The western part of Manasseh is located southwest of East Manasseh, north of Ephraim extending from the Jordan River to the Mediterranean in between the Sea of Galilee and the Dead Sea. Manasseh's western lot is divided into 10 portions. One of these portions is given to the daughters of Zelophehad, who were given permission to inherit ensuring Zelophehad's name continued. The back story for these women is given in Numbers 27. Looking at the map and back to Joshua 12:24, it is interesting to see that at least one town appears to have been named after Zelophehad's daughter Tirzah, just as Gilead was named for Machir's son.

Like Ephraim, Manasseh does not drive out all of the Canaanites.
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Extra Land

Photocredit: Holman KJV Study Bible pg. 391

Ephraim and Manasseh complain about having only one lot split between them. Joshua tells them to take the mountain and the land of the Perizzites as well. The men of the tribes are afraid and doubt their ability to conquer the Perizzites who are said to be giants with iron chariots. Joshua reminds them that if they have faith in God, they will be successful.
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References

1. Henry, Matthew. "Joshua 16". Bible Study Tools. 2014
2. Gills, John. "Joshua 16:10". Bible Study Tools. 2014