We have an integrated profit sharing plan (integrated on the taxable wage base), but use compensation only for the period in which a new participant is eligible for the year. If a person is onlly eligible for 3 months of the year, should we be using 1/4 of the wage base for his integartion level, or do we use the whole wage base for everyone?

Doesn't the plan document address this issue?

The only time that you would alter the integration level is when you have a "short plan year". If you are working with a 12 month plan year, you would use the full integration for all participants, regardless of what their comp is.