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You are using 'in' twice in each sentence; in the first it doesn't work because it is redundant (with the 'in' of 'into'); in the second it is OK, because the 'in' in 'effort in doing' means 'involved with' . Do this:
1. We've put a lot of effort into developing this project.
2. They believed they did not put in / put much effort in preparing for the test.