The PowerChurch database is designed to handle a large number of individuals, so splitting this up into 2 database files would probably be overkill.
One way to handle what you are talking about is to use some of the options on the family, in addition to use of the codes.
For example, if you have a family that you want to keep in your database but don't ever want to see them on a report there is an option on the intergrated data screen (or family mailing list) to include in Membership module reports. It is located in the lower right hand corner of the screen, and when unchecked this family and its profiles won't appear in any reports.
If that option is to drastic and you want to be able to sometimes see them and sometimes not, create a family code and/or a profile code called inactive (or whatever you want to call it) and assign it to that individual. now whenever you run a report you will have the option of unchecking that status code taking the family or individual off of the report.
It also needs mentioning, family codes affect family reports and profiles codes affect profile reports.
obviously neither option above will affect locating families because they will all still be there, it will however take care of the report problem you described.
Hopefully this information will help you.
Feel free to forward any suggestions you may have to firstname.lastname@example.org