Decide whether to do any in-office testing
Many commonly performed in-office labs can now be performed by the patients themselves using home testing kits. This is includes HIV, Hep C, Strep, and UTI diagnostics, as well as lipid panels, TSH, HgA1c, PSA, and Vitamin D tests. See a more complete list of offerings here.
Though home testing is an increasingly good option, these kits can be frustrating and time-consuming for patients, and home kits don't exist for all CLIA-waived tests (see full list).
To do CLIA-waived tests: file for a waiver
To get waived, fill out a CMS-116 form and submit it to your state's CLIA Agency (lookup here). Some time later, you'll receive a "remittance coupon" detailing how to pay the certificate fee.
As of 2014, the following states have additional requirements surrounding physician-office lab tests: AZ, CA, CT, DC, FL, LA, ME, MD, MA, MI, NV, NJ, OR, PA, WA, and Puerto Rico. Do a Google search to figure out what else you have to do.
Washington State residents: you should fill out this form in place of the CMS-116 and mail it to the listed address.
Consider offering physician-performed microscopy (PPM) services
PPM is the next level up from waived status. It lets you do all waived tests as well as these microscopic procedures. However, this requires compliance with multiple subparts of CLIA regulation (Patient Test Management, Quality Control, Personnel, Quality Assurance, and to some extent Proficiency Testing) and is probably not worth the trouble, especially early on.
Maintain best practices
Check out this strangely colorful document from the CDC detailing best practices for CLIA-waived facilities. How much of this you decide to implement depends mostly on your risk tolerance - any CLIA-waived facility is subject to random audits, though they are rare.
Set up a reminder to renew your waiver every two years
FollowUpThen is a great free service for scheduling email reminders.