It's pretty easy to organize your sidebar or move files in Paperless to a new file or to archive information. There are a few ways to skin this cat. Here are some options:
The sidebar in Paperless shows your "Library" (where all your documents are shown), your Inbox (items not marked as done). It also shows collections, smart collections and folders (which can contain collections or smart collections.
One thing to remember is that collections and smart collections aren't "physical" locations - just views of items in your library.
To further organize your sidebar you can drag and drop items around, you can hide or show groups using the controls next to their names.
Moving your files to a new file (splitting up a Library):
Libraries are the document that stores your info. Sometimes you may wish to split items or groups of items into other files or maybe just better organize things. One example is if you have lots of receipts, in your library but keeping your home business expenses separate from your personal expenses is better for bookkeeping.
If your Library file is setup the way you want it (custom fields etc.), one idea is to make an empty clone of your file to store the new data. To do this simply go to File>New Library and then when prompted you can see a selection to base the Library off of another library. In this example, let's say we are splitting the Library by year (a popular thing to do). Save the new empty clone as "2017.paperless" and then you can drag any 2017 items and drop them into the open Paperless window. - this makes a copy of all the items and retains the metadata. Once you are comfortable and make sure you have backups of your data, you may wish to delete the documents from your original library. repeating this process you can split your file into several by year. i.e. 2017, 2016, 2015, etc..
When doing this "clone' method you'll still have all the smart collections from the original file as well as collections (but they'll be empty until you re-populate them with the ad hoc list of items you wish for them to display).
Another way to split up a file is to go into the MacOS Finder and then make a few duplicates of your Library File. Open them in Paperless and delete the items you don't wish - for instance, for 2017, you could delete all but 2017 files. Then close and rename the library "2017.paperless". repeat this process and you can have 2017.paperless, 2016.paperless, etc.. The upside of doing this method is that you retain everything from your original file, collections, smart collections, view settings, etc..
Yet another Option is to archive (make a compressed zip of your Current Library) and start a fresh library. Some people like to do this because maybe they are getting a lot of false positive matches for merchants or they have an onerous amount of smart collections slowing down the file or they are experiencing some odd occurrences with their current file. whatever the case, a nice tiny fresh file that is super responsive and only contains new info from that day forward can be a nice option. when creating the new lirbary chose things like whether to import the default list of merchants or categories. those have a big role in whether you get a lot of "matching" and or false positive matches. That being said, adding a few items on a blank file will make it more likely that you'll have a match for the merchants you frequent. So, in a hybrid model, you could make a blank file but then drag over some items from the old library - this will populate the merchants and categories, etc. but only for those specific merchants.