You should do two things:

• Decrease the “Value of One Stock Option” entry on the assumptions/investment/options screen. You'll have to play around with this value until you get approximately the right distribution on the cap table. For example, changing the “Value of One Stock Option” from $.01 to $.001 will result in ten times as many options being granted; changing it from $.01 to $.0001 will result in one hundred times as many options being granted, etc. You should have to do this just one time to calibrate the model based on all the rest of your assumptions (like number of founders' shares, values of option packages to employees, your desire to distribute equity among the three classes of shareholders, etc.)
• Increase the “Values of Initial Option Packages” received by individual employees on the assumptions/costs/personnel/employees screen. This will increase ownership positions for just these employees.

Related Questions:

How do I see the cap table?

How do I determine if my cap table is reasonable?