A good resistance training program will fortify and strengthen your body, reinforce your core, and help you to gain proficiency and coordination in moving both external objects and your body as a whole; this means that, whether you're hiking uphill or planting perennials, your body will listen to your commands more readily and respond more positively and efficiently.  Bulking up is usually associated with a fitness regimen that includes heavy lifting accompanied with an expanded caloric intake.  A good trainer will design a program specific to the needs of the client, and consistent with their fitness level, goals and experience.

In my experience, it is a lack of proper technique that leads to pain in the joints.  Done properly, squats and lunges are the best medicine for your knees.  A good training protocol would include a progression of exercises that prepare the body for the demands that the squats and lunges pose.  The discomfort associated with these exercises is usually not a weakness in the body, but a lack of proficiency and an improper progression rate which results in you doing exercises before your body is ready to handle them.