That's all you can do. Just remember that before you introduce new but different genes, make sure your line breeds true. You don't want the new gene/strain to be dominant over your line.
When making a new or unpopular strain, It is best if you at least start with 2 pairs. Keep the lines separate until you need to introduce new genes. This should insure you don't lose your line. And once your line really breeds true, crossing them to new genes shouldn't be a problem.