Changing the number of registers downwards can be a bit confusing. Here's how to do it.
Log into your account, and click the "Settings" tab, and then click "Account Settings"
Then click the "Change" link

That will bring up this screen, where you'll get the drop down that will let you add or subtract registers from your base number

Select the decrease in registers needed (the account in the image has one extra register. Setting it to zero will mean it has the base number). That change will take effect during the next billing cycle. The current billing cycle will still charge you for the registers you have. Please email support@shopkeep.com for any further help.
Note that, when you add in a register, you are shown this text:
Adding additional registers will end your evaluation period and you will be charged at the end of the period for using those registers even if you cancel your account before the 30 days are up.
If you would like to end your Evaluation Period and add additional registers, please click the Enter my Payment Method link below. After we have validated your card, you will be returned here to complete the process.
Please click one of the links below to let us know what you'd like to do.
Shopkeep is not responsible for charges incurred after ignoring this warning, as we hope it is sufficient.