So u can either read the books in order of publication, preference, series wise or chronologically.
There are three main series:
The Infernal Devices, the Mortal Instruments, and the Dark Artifices. Accompanying them are the Last Hours, The Eldest Curses and The Wicked Powers (TWP is still in the works)
The best way according to me is to read first The Mortal Instruments, then The Infernal Devices. Then you read Tales from the Shadowhunter Academy, which is an accompanying book. After this you read the Dark Artifices. Then Red Scrolls of Magic (the first in the Eldest Curses. The second is coming in Sep). Then u can read Chain of Gold (First in The Last Hours) and The Bane Chronicles can be read whenever after TMI, and Ghosts of The Shadow Market any time after TDA.
Hope this helps!!
And it's not a trouble at all!! A lot of people are confused and Clockwork Prince is amazing!! I love Tessa