As a first time tech entrepreneur, I was confused if I should select one tool for mobile prototyping and other tools for implementation. I wanted to deliver my mobile app service as soon possible but I don't want to make mistakes when selecting tools. I have seen tools like Appcelerator, https://codiqa.com/ and PhoneGapp. Other than that should I also develop for android and iPhone separately, or should I use one of the above tools to develop once and deploy in different devices? Time and money is also a constraint for my startup. Please advice me. Thanks.
I also would recommend @AlexJubien's advice about familiarizing yourself with different types of wireframing and prototyping.
PhoneGap would be used for producing real consumable software by users/test users (from your original question, for your 'implementation" phase). Sure you can generate high-fidelity prototypes with it, but that would be similar to building out a full website just to test or validate an idea.
If you need something to simply test out your idea and show users what your concept is like, you can go with something as simple as Balsamiq or Omnigraffle for basic wireframing and click-flows, or something more highly interactive/hi-fidelity via Axure or an online prototyping such as Proto.io or Fluid.ui which would allow you to drag and drop UI elements (similar to Balsamiq) but also export your prototype for interactions with your users on desktop and mobile (e.g. https://showcase.proto.io/share/?id=c86aa62b-21b6-4c9f-9eff-acf7896a2368&v=6). Another level of prototypes would be click-flows with a service like Invisionapp.com using actual designed pages (e.g. screenshots, PSD exports, etc) of your site with hotspots linked to give your users an idea of general flow and functionality of your product.
I think that's the general misconception about wireframing and prototyping, and learning more about that will give you some valuable insights about what you need in order to validate your product and help with building it.