I am having some problems when I want to add custom jQuery code that affects the form.
For example when someone clicks an input or radio button another input or element
Not sure if you need help with this any more as it's been some time since you posted your question, but this may help others in the future. I had the same/similar issue with not being able to run JS/jQuery on the Ninja Forms and found that it's because Ninja Forms load their forms asynchronously. So, when your document.ready function runs, the form doesn't yet exist and it's not able to bind.
Ninja Forms have their own event ready state that can be used as follows:
jQuery(document).on( 'nfFormReady', function( e, layoutView ) {
// Your code goes here...
});