Not sure what you mean by "all over the place." If you mean that you have too many screens with one or two apps on each page, you can simply consolidate apps on fewer pages by "long touching" an app and moving it to the edge of the screen. The iPad will then move to the next page and you can "drop" the app there. Repeat until you eliminate all the apps on a page and the page itself will disappear.
If you mean that you have screens filled with apps you'd like to "consolidate," simply drag one app on top of another. The iPad will enable you to create a "folder" that holds both (or many) apps. You can name the folder whatever you please.
If you mean you simply want to rearrange the order of apps (or folders) on a single screen, simply drag the app between two others and drop it. The iPad will rearrange the apps to reflect your placement.
What you CANNOT do (at least on a non-jailbroken iPad) is to depart from the rigid grid structure imposed on the placement of apps on a page. For example, you cannot place two apps on the first row and four apps on the second row, etc. The iPad will fill a row before allowing you to put apps on the row below it.
Finally, you asked how to "automatically" rearrange your apps. Ain't happenin'