Dynamic Forms And Updating On Reload, Inserting Functions, Jumping Text?

I'm trying to create a dynamic form, and for the most part it's working out fine.I'm using javascript with onclick and onchange on checkboxes and select boxes to change the form as the user makes selections.However, there's a few issues I'm running into that are giving me problems.

One is that when the user reloads the page, all of the javascript inserted or removed form elements are reset, but the choices on the checkboxes and select boxes aren't, which looks very strange to the user. How can I avoid this? I'm currently including scripts tags in the body of the html, but this is pretty messy and hard to manage. Is there a better way? Second is that I'd like to be able to insert javascript function declarations into text that is dynamically inserted by javascript.However, when I do so, the browser does not recognize the functions. The reason I'd like to do so is that I am using Ruby on Rails, and would like to be able to keep the scripts in the partials to which they relate. I have to use inline javascript, because the scripts are having element ids inserted based on Ruby variables. Is this a lost cause, or is there a technique that enables dynamically inserted javascript to be loaded?

Lastly, my dynamic form's javascript shows or hides portions based on what it encounters while loading. The main reason is that I want to show the whole form for users without javascript, and then hide advanced or obscure details unless they are activated with a checkbox on the form for users with javascript. However, this is creating a jarring pop-in effect, where on first load, the pre-javascript formatted page is shown for a split second, and then the javascript kicks in and fixes everything and the page visibly jumps and changes. Is there a way to avoid this to create a more polished effect?