In Python you execute the code line snippet `import sqlite3` which imports the sqlite3.py wrapper, which in turn imports the compiled extension (pysqlite2) with the name _sqlite3, which in turn loads the standard dynamic loadable library sqlite3 created by the compiler (and/or shipped with Python).
The particular filename extensions and locations vary based on the Operating System and version of Python, which you have not provided.
Basically, in order to have the Python pysqlite2 (sqlite3) extension use a version of sqlite3 that you have compiled yourself, you have to find the version of the sqlite3 dynamic load library that is being loaded and replace it with a compatible version that you have compiled yourself -- this may also include issuing magical incantations to your Operating System to *make it so*.
The sqlite3 executable is, strangely enough, an executable. You cause it to be executed by a Python program in the same manner as you cause any other executable to be executed in the Python environment -- by using os.system or other method for executing executables.