Hi rver,
Following up on what bigpup has said, when a Save takes place everything then in Random Access Memory with one exception is written to your SaveFile/Folder. The exception are those temporary files Puppy writes to /tmp. By everything, we mean EVERYTHING: the mistakes you made, the applications you installed which didn't work; and the junk files and malware you didn't realize you were picking up while you surfed the web. Moreover, with the Automatic Save turned on, a power-surge or outage can corrupt your SaveFile/Folder if it happens to be performing a Save when that occurs.
I discuss all the repercussions of turning off the Automatic Save in this post:
http://murga-linux.com/puppy/viewtopic. ... 066#974066. But, besides turning it off, there are two things mentioned I strongly recommend: move the /my-documents folder out of /root onto /mnt/home and move the /.mozilla and /.moonchild productions out of /root onto /mnt/home. The cited post explains how: it's easy. By doing so, your browser Bookmarks will automatically be preserved when you make them; as will the word-processing and other data files you create in the my-documents folder.
Depending on how much RAM your computer has, it may also pay to move the .cache files. They are not on your computer for your benefit. They are placed there so that Web-servers don't have to transmit them again. While in /root they are using RAM leaving less RAM for you to do what you want.
Unfortunately, after that post was written it became necessary to build google-chrome and its clones to be run as Spot -- a limited User located either in /root or /home which is another location occupying RAM. As a limited User, files relating to it can't be moved, as Spot can not access the rest of your computer. [Mike Walsh has published an application for easily transferring files into and out of Spot]. But bookmarks and addons can only be preserved by executing a Save.
My preference is to install applications, change settings and load/unload SFSes immediately after bootup and execute a Save before I begin surfing the web. But with Google-Chrome & clones now occupying /root or /home, I'll make a note of desired changes to them, shut down, reboot, then make changes to them and Save before surfing elsewhere.
With Google-Chrome & Clones, I install the addon "History Eraser". You may not want to actually erase your history. But one of it's settings clears cache.