1)
What is the meaning of "va'Yasa ka'Tzon Amo"?
1.
Radak: He caused them to leave Egypt after the firstborns died, and He caused them to travel slowly, like a shepherd conducts his flock. Malbim - also they followed Him like a flock follows its shepherd.
2)
Why does it say "va'Ynahagem ka'Eder ba'Midbar"?
1.
Malbim: In the Midbar they were like a flock that finds its pasture there. So they found their sustenance - manna and water of the well.