Create a results page on your web site. (In one of the following steps you'll add code to display Custom Search results on that page.)
Go to the CSE control panel, click "Look and feel" in the sidebar, select the (so-called) "Two page" layout option, and click the "Save & Get Code" button.
In the first text box under the heading "Specify search results details", enter the URL of your results page.
Use the first provided code snippet for your search box(es) (e.g., in your page header).
Place the second provided code snippet at the location where you wish to display search results on your results page.
The "two page" layout's results code will display a second search box above search results. If you've placed a search box in the page header, the second search box above the results may be redundant. You can proceed as follows if you wish to remove the second search box:
Go to the CSE control panel, click "Look and feel" in the sidebar, select the "Results only" layout option, click the "Save & Get Code" button, and use the provided code on your results page (replacing the previously installed results code).