I try to put a door and RPG Maker sees it as being the same layer as the building so it replaces the building tile and the transparent part shows the ground:
http://postimg.org/image/5z67ouoi7/
That frame in the picture isn't a door, it looks like a window frame.
You have three layers in RM - bottom layer is for the autotiles (A-Tiles), and that is where most of your ground and walls should come from.
middle layer is everything from B to E tiles, that's usually used for decorations and those parts that you do not want as autotiles.
top layer is the events (although events themselve can be placed below, above or same as player, all three options are above the middle layer).
Events are used for animations (by using sprites, not Tiles) - that's what is used for most doors, because only with sprites you can animate a door opening and closing, but it's also used for animated fire columns and the like.
Events are also used for decorating above the B-layer, for example to place decorations on a table (BtoE-Layer) which stands on the ground (A-Layer).
I think you should practise with some mapping tutorials first, that should tell you what the different tilesheets and options are used for.
If you follow the link in my signature, you'll get links to other tutorials like one on shift-mapping, which is probably the most important tutorial on mapping that exists (it teaches you about the results of using the shift-key when mapping with autotiles)