Create your own supplementary book
I have created my own supplementary books when I did not want to risk damage or modification to the primary books.
With created supplementary books, you need to be careful how you organize them. If your own errata book has, on page 2, an update to your source book's chapter 3 page 45, you could easily forget or miss the errata. At that point it's as good as if you didn't have the errata.
Whatever version you use below, keep the entries in order. If you have to make updates, try to write updates in where they should be in the correct order. If you can't, you will need to remake it.
If you can use a laptop to help assist your game, this is a great use for it. A word document which properly uses headings so that you have an automatic table of contents that you can just click on to see what you need works great.
If the amount of errata is small enough, try to fit it all onto a single paper.
If you are printing this, use tiny page margins, single-spacing, waste no space on the paper. Try to keep entries to 1 line if you can, and make the source-book's topic and chapter/page number bold.
Ch1, p5 Widget Care and p6 Sprocket Care: Change "month" to "year" and "peanut butter" to mustard"
Ch 3, p45 Foobaz Results: add "unless already buffed, then choose this or the other buff, not both"
This can still work if it flows onto a second or third page, but eventually
If not small, include a listing of source-book errata locations on the errata-book's cover page
Best shown by example.
Source-book chapter 1, page 5:
Widgets are cool things that do stuff.
Turn them upside down to make them go.
Cover them in peanut butter once per month.
Source-book chapter 3, page 45
Foobazzing is the thing people do to improve efficiency.
How to foobazz:
Sing "Mary had a little lamb" while holding a Widget in your left
Efficiency is improved 50% for all actions.
Errata book cover page:
Errata for Player Handbook
Ch1, p5: Widget Care, p7: Sword Use, p7: Shield Use, p10 X
Ch3, p45: Foobazz results, p50 Y
Errata book page 1:
Player Handbook Chapter 1, Page 5
Cover them in peanut butter once per year.
Errata book page 3:
Player Handbook Chapter 3, Page 45
Efficiency is improved 50% for all actions unless they are already
affected by an efficiency bonus, in which case you may choose which
bonus to apply but not both.
Those entries could have been on the same page if they fit and that makes you happy, but I'm assuming there are other errata that might be on the page as well. Even if they would fit, it doesn't hurt to leave some empty space to write in more errata later on.
If the company adds another section about Widgets or changes something else in chapter 1, it would be nice to include that on errata-book page 2 instead of adding it to the end. Just remember to also add ", p6: Sprocket Care" to your cover-page line so it reads "Ch1, p5: Widget Care, p6: Sprocket Care"
If you get further errata to the same section, you can just cross out and write in whatever you need. For example, if a later source-book change makes Widget Care require mustard instead of peanut butter, then you just cross out "peanut butter" and write "mustard" so the line in your errata book reads "Cover them in mustard once per year."
If you have multiple books for which you want to keep track of errata, you can have one errata-book for all of your rulebooks as long as all of the "ChX, pY: Topic" summaries fit on the errata book cover page.
Some other tips to go along with this
If the errata book gets large enough that you can't find the page you need quickly, make it easier to find a specific section by making it stand out. Ways to make it stand out:
Use sticky notes where the sticky part is facing the bottom of the page and the non-sticky part is poking up out the top of the page, and write the section on the part sticking out. Eg: GM Guide, or Chapter 3.
Similar to previous point: do something to make tabs stick out the top. You can buy items to help with this from office supply stores, or you can offset a page so it's a half-inch higher than the others and cut off some excess so it forms a tab. Write on the tab.
Fold the corner of the page of a new section over, and write the section-name (GM Guide, Chapter 3, etc.) next to the folded corner. The corner helps you see where sections are, and writing next to the fold means you don't have the open that page up all the way to see what it is about.
You can also write errata-book's page numbers on its cover page summary and write page numbers on all the pages, but if you do that then you're stuck with specific page numbers and can't easily rearrange your errata book when more errata comes in. Write page numbers if you don't expect much future errata.
Other supplements, not just errata
This method also allows you to include whatever other supplemental additions you want.
Ch 4, p70 Types of Terrain
Homebrew additions to this table: Mushroom Forest, Moon, Lava Lake
Ch 5, p80 Spells
Bob is using the following spell from the "1 Million More Spells" book, but his sister is borrowing it so let's record it here:
Lightning Scorcher: Requires 1 metal rod and 1 battery. Blasts everything in sight for 10 damage.
Just make sure that any time you reference a source book that you have your errata page or errata book available too and that you glance at it to see if there is something for the section you are reading.
This method is the best balance I have found for leaving the source books in the best condition possible, referencing as much errata as you want, knowing fairly quickly if there is errata for a certain spot, including all sorts of supplemental info not just errata, and finding it quickly enough that you don't start to ignore it.