Margy, sorry I didn't get back to you sooner, but things got a bit hectic and your response kinda got away from me.
I'm not sure how to tell if the nematodes you have are the good or bad kind without a soil test.* That might be helpful in your situation.* Just because you didn't bring them in doesn't mean they are bad ones.
You mention that crop rotation is tricky in a small area and I have the same problem with a tiny veggie garden.* I often will plant my tomatoes (required by my hubby to grow yearly)* :) in pots and move them around the garden.* Something that might work for you would be to plant companion plants that repel the bad bugs or even attract the good ones.* Here's some helpful sites about companion plants.* The last site is for herbs.
When weeding, the best way to make sure you are removing a weed and not a valuable plant is to pull on it. If it comes out of the ground easily, it is a valuable plant.