I just installed Hearthfire and am planning to purchase Lakeview Manor. This is my first time playing Hearthfire, and I know nothing about it. Spoilers welcome.

My first question is, if I just build the first, basic part of the Manor, later on, when I upgrade and add on to it, will it reset my storage containers, or cause any of them to disappear?

Your basic house layout will be unmolested when you decide to build the main hall. Your container contents will not reset.

Once you build the main hall, you will get the option to convert the basic house into an entryway. This will still leave the contents of your containers intact; however, doing this *will* delete one container: The satchel on the shelf near the northwest corner. Converting removes that shelf and everything on it. So just make sure that satchel is empty before converting the basic house to an entryway, and you should be fine.