Sometimes, I get confused as I add more and more ideas and scenes in a plot, is there any way of arranging these?
Buy a bunch of 3x5 cards and write plot elements on them, then organize them into a line or a tree or some other visual representation that makes sense to you. Play around with orders: put everything chronologically, then put it how you intend to tell it. When doing this, you can also decide what not to tell by removing cards and seeing if the action still makes sense. You can use highlighters to color-code different cards: either by character or by importance or by storyline, or whatever criteria you feel is necessary.
Keep in mind, not everything that happens needs to be known to the reader. It might make things easier to write if you can figure out how to decide what they won't see. Certainly make cards for every event that happens, but remember that just because you made a card does not mean you have to write about it in the story.
You could try using a simple spreadsheet. Use the rows to represent characters or events and the columns to represent time frames or locations. You can put each of the elements into place to get a visual representation of your story flow. This will not only help you to develop a consistent timeline, but also to make sure that you don't have any characters showing up in two locations at the same time.