I can relate to your situation almost exactly (except C #).
This is a very subjective question as to which is better, because it all depends on your exact settings, circumstances and requirements. I'm still pretty new to deciding what works best for the project, but based on my experience, I can tell you what I did.
We went with the N-level configuration so that we could separate the user interface, logic and data. This will make it easier for us to maintain code with an additional separation of problems.
We went with Masterpages (using WebForms) so we can work on the consistent look and feel of the application. You can further customize themes with themes, as well as your standard CSS and Javascript. You want to easily manage the layout and not force yourself to copy / update the code on each page.
When Javascript arrives, itโs usually best not to use it directly on the aspx page itself (if itโs not very small), since you will use caching in the browser, plus you can also minimize the file to speed up / simplify the downloads. I personally recommend using jQuery for the platform, as it is easy to work with, has a huge community and is well documented.
These, of course, are just a few of the things I have done. It doesn't matter if it helps you or not, it depends on your circumstances. I still have a long way to go, and I personally try to read as many blogs as possible on topics that interest me, if possible, teach videos or just ask focused questions here (if you cannot find the answers). There is plenty of good information and many sample applications that can help you learn new design patterns and techniques. After all, there is no absolute โrightโ or โbestโ way. :)
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