Use your pop color(s) sparingly, but repeat its use throughout your site to help create repetition. For example, on this site the pop color is the lime green and it is used for illustrations and icons. 

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Your main color(s) should be used the most. Use them as backgrounds for sections and headers, or consistently as titles to sections of content. Work them in on every page so you create the specific look and feel you were going for when you selected the colors.

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Your neutral color(s) can be used for your text if it is not too light to read against the page background. Otherwise you can work it in where it feels like it fits. On this page, the neutral color is used as a section background to separate content.