More than one way to perform the function, do I have to patent them all? How?

Your good question invites a detailed response. I don't have enought time to respond fully, but I will offer a few thoughts. First, the answer depends on whether the system you mention (and presumably claim) is an apparatus or a method of doing something. If the claims are to an apparatus, then it is the apparatus that is protected, rather than what it is used for (an a different manner of apparatus would not be covered). If your claims are to a method, then it is the steps of the method that are covered. If the end result can be accomplished using an entirely different (second) method, then the second method would not be covered by the claim for the first method. However a patent application might claim both the first and second method, provided that the written description discloses and enable both. In this case the patent office might decide that each method is a different invention and require you to file a second application (but the second application will have the same priority date in this fact pattern).

You question is an excellent question. Many inventor represent themselves and do not seek the assistance of competent Counsel. It is one of the great misconceptions of Patent Law that everything that is novel that is disclosed in the Patent is protected once the Patent issues. To constitute a Patent Infringement, an Infringer must infringe at least one of your Patent Claims. It is critical that you obtain all of the Patent coverage that you are entitled to, and not leave any scraps on the table for your competitors. Once the Patent issues, your competitors will read your Patent and they will look for any loopholes in your Patent Claims. They want to use the essence of your Invention without Infringing your Patent. I strongly urge you to seek the assistance of competent Counsel regarding your invention. I hope that this helps.

You have touched on the reason to carefully select your patent attorney. Your patent attorney should be drafting claims directed to your invention that not only cover your preferred commercial embodiment, but also alternative embodiments in order to reduce the possibility that your competitors can design around your patent. The scope of your patent claims should only be limited by the prior art. As always, it is advisable to consult with an experienced patent attorney to discuss your intellectual property rights and how best to protect them at your earliest opportunity to do so.

You will be best protected if you describe all of the ways to make the system perform the desired function. Your patent application must teach how to make and use your invention - giving sufficient detail that anyone can make and use the invention. Your patent application must also teach the "best way" that you know how to make and use the invention. Putting it all down on paper is not hard - and that will allow your attorney to broadly claim your invention to prevent copying by others. GOOD LUCK!

If there are significant differences between the ways to alter the system, then you would probably need to patent each one individually. However, if there are just some simple variations between the ways to do the job but the outcome is always the same, you might be able to include all the variations in one patent application.