Hi AOB9,
first of all, congratulations that you finally took the big step and start to move from the PC to the real airplane. You will find that using both of them will have it's merits and will help you in your training, as well as the skills you have acquired over the years will not be in vain.
My own experience goes back to 1983 when I did my PPL and had my first flight sim on a device called the Sinclair Spectrum. Since then, I have worked in the field, the last 13 years as an editor for a german based mag. (So Pace, it's well possible I know you
if you've been working with Rob and his great folks, or better you are one of them.)
First of all, FSX or 2004 are like ANY training aid. If you use them "unattended", that is without a syllabus or at least a teacher to tell you how to use it, things will happen exactly as you describe. You will acquire "bad" habits, out of lack of knowledge. If, however, you are using it in combination with the real life checklists and procedures you now use when flying your real plane, and the sim is brought up to a certain level, you will find the help invaluable. Many flight instructors sneer at this, but in that particular case, I beg to differ out of experience.
I stopped flying for real in 2001 and restarted last year to regain my SEPL and will also regain my IR eventually. I never stopped flying the sim however, it was (and is) work after all, and this did help me a lot when I restarted. It did help that there was a professionally made addon available for the plane type I am flying (and own now) and that I have a photo-realistic scenery for the whole of Switzerland and Southern Germany, where I was training.
What did help was that I could train the procedures and checklists, memorize speeds and do the VFR navigation parts before each flight. Both only work if the model and the scenery are up to speed. If you are training on a C172 which is close enough to the FS 2004 variant, then you are fine there. What will help is if you do get the photoscenery for the part of the country you fly in, especcially if you later on want to train the navigational flights. There are such sceneries available, pm me if you can't find them.
If you do this, there is no need to unplug your joystick and pedals. Treat each FS flight as if it were a solo flight session, use the original checklist and if you want to go a step further, get Track IR, which for VFR is a very good tool.
I can tell you that last year I did a demonstration for a colleague of mine who is an FI and who knew not much but prejudices against FS. I borrowed a system running Switzerland Pro X on a 42 inch TV with Track IR and demonstrated it at an FI meeting in that school. Since, they have acquired an equal set up and are using it to great success to prepare their students for cross country and for other things.
Now that I am flying again regularly with my high performance single, I still will prepare and fly each flight to places I have not been to and I do find it will give me a lot of free capacity during the flight itself. The key to this is, as I said, the condition that you use the absolutely same checklists and procedures as in real life as close as possible and that you don't shy away from getting the best appropriate addons for what you need.
So do enjoy the experience of getting your PPL, you'll see how great it is once you are there. If there's anything I can help, feel free to pm or ask here.
Best regards
AN2 Driver