user is the time that the CPU spent executing code in user space (i.e., in the database itself); sys is for code in the kernel.
When doing I/O, the CPU spends most of the time waiting.
Sufficiently recent versions of SQLite also show the elapsed real time:
SQLite version 3.8.6 2014-08-15 11:46:33
Enter ".help" for usage hints.
Connected to a transient in-memory database.
Use ".open FILENAME" to reopen on a persistent database.
sqlite> .timer on
sqlite> UPDATE ...;
Run Time: real 36.591 user 17.362911 sys 1.809612