I, personally, would base the employees' wages on my needs for that employee to be certified and any value that such certification would provides to me and to my practice. On the other hand, if it's your desire to provide a bonus for board certification (something that neither you nor I currently get from our payors) as a means or reward or retention of an employee, the first thing to do is to determine if it is a one-time bonus or an ongoing per-hour bonus. It appears that it is your established policy to have it as an ongoing per-hour bonus, in which case the total raise should be 3% of the employee's hourly wage (for cost-of-living/years of service) PLUS the $1.00 per hour for getting boarded PLUS any other bonuses/rewards.
Additionally, I would calculate the company's cost of medical insurance as a percentage of the hourly wage for each employee and let each employee then know how much per hour is contributed by the employer towards the employee's health insurance as well as the percentage increase from year-to-year of that benefit as an itemized amount and also as factored in to the hourly wage equivalent.
You could also factor in vacation and holiday pay, employer contribution to 401k/pension plans, the employer share of the payroll tax deduction (Medicare 1.45% of wages plus Social Security/FICA 6.2% of wages) plus any additional amounts paid on the employee's behalf and add to the total wages and benefits and calculate a total dollar-per-hour-worked amount. A bit of calculating the first time around, but then just set up a spreadsheet and plug in the numbers for each employee scenario on an annual basis.
It never hurts to let the employees know the total COST to your practice of their employment. They will get a better appreciation of the VALUE of the job that they have and the cost to you. Employees often lose sight of anything but the hourly wage.
For example, an employee making $20.00 per hour, working 40 hour per week, with 4 weeks of paid vacation per year, plus six paid holidays (New Years Day, Memorial Day, Labor Day, July 4th, Memorial Day, Thanksgiving Day, Christmas Day), plus taking 4 paid sick days per year, plus 2/3 of the cost of single-person health insurance premium paid by employer, plus 15% of wages contributed to retirement plan, plus 7.65% of wages as payroll taxes paid by employer would really cost the practice $29.76 per hour worked--almost 150% of the hourly wage. For employees offered a family plan for health insurance coverage paid at 2/3 by the employer, the hourly equivalent would be $33.43 per hour, or 167% of the hourly wage. [Health insurance rates based on Kaiser/HRET Survey of Employer-Sponsored Health Benefits 2012,
http://ehbs.kff.org/?page=charts&id=1&sn=6&ch=2650, http://www.pmanet.org/?cmd=main.content&id_content=2142627292]
Obviously, the actual per-hour-worked wages will vary based on the hourly wage and benefit package provided including the number of weeks of paid vacation, paid sick days taken by employee and the cost of health insurance and employer contribution, but as you can see, the total wage and benefit package provided can be substantial as a percentage of hourly wage, fact often overlooked by employees and by those who say "you didn't build that."