Neither construct does what you want.
You are using the latter part of the sentence to expound on what is said in the former, but the way you have worded them makes them disjoint, so you cannot use subordination or co-ordination, or even divide them into separate sentences.
Separate them with either an n-dash or a colon, and either keep the second instance of "in" or allow the reader to carry the first instance across:
The power of a programming language lies in abilities of the programmer using it -- in how effectively he is able to break down the program and glue the solutions together.
The power of a programming language lies in abilities of the programmer using it: in how effectively he is able to break down the program and glue the solutions together.
The power of a programming language lies in abilities of the programmer using it -- how effectively he is able to break down the program and glue the solutions together.
The power of a programming language lies in abilities of the programmer using it: how effectively he is able to break down the program and glue the solutions together.