If you put your hak above the original in the toolset, it only needs to contain any files you have changed. They will override the original files.
Alternatively, copy and rename the tileset hak. Replace files with your versions. Now you only need that one hak in your module.
Pros and cons - if you are using a lot of custom content, players may find it easier to download your module if everything is in one hak on your module page. Also, you are not dependent on the availability of other pages with the original haks. On the other hand, historically, players didn't like to have to download umpteen versions of large haks (less of an issue now that downloading is fast and disc space is cheap). If the original hak is a very popular one, players probably have it already, which is another reason for the top hak approach.
If you're adding tiles, you will need to put new versions of the .set and .itp files in your top hak.