By

When we describe the method to do something, we use by + verb (-ing form):

• You can open the package by cutting the seal.
• You can study English by watching series and movies.
• You can cut wait just by running.

With

When we mention the instrument used to do something, we use with + instrument's name:

• I'll just cut it open with a knife.
• I like eating chicken wings with my hands.

Note: We can also use by when referring to means of transportation or anything related because that is the method of transportation:

• We can go by car if you want.
• Are we going to travel by sea or by land?