All out citation styles come from the public repository at citationstyles.org and they also have a visual editor: http://editor.citationstyles.org/searchByName/
You can find your style, edit it, and then in Paperpile go to the cog --> Settings --> Citation Style to upload your edited style. It will immediately be available in google docs.
The styles can be fairly complex and can take a while to wrap your head around, but with the visual editor you can generally click the bit of the citation you wish to change which will bring you to the relevant variable. It sounds like you want to change the "text-case" attribute to Sentence Case, or Lower Case. Once you have edited the style be sure to examine the tree on the left for alternate cases. For example , if there is a conditional further up the tree, you may have only edited the sentence case for articles, but not books. Different citation styles use different conditionals to separate their formatting rules, so there's no hard and fast rule here.
When you're done, change the Title of the style under "info" in the left panel. To save the style click Style --> Save Style, above the left panel. It will prompt for a change of the style URL, accept this, and in the orange box that opens, click Save to Disk. Then upload it to paperpile as described above.
Let me know if you need further help.