With v1.x of SMF, mods only install to the SMF default theme. (Although, some will install to Babylon and Classic, too).
To make them work/show with custom themes, you need to make manual edits to the relevant files in the custom theme's directory.
To see what those edits are, you need to look on the mod's page.
Just below the download link, you'll see a parser.
Select the version that you're using and click "Parse".
Clicking "Select", just above a block of code, will select the code, with it's correct formatting.
Then, you just need to right-click and select "Copy".
When you paste the code to where it's supposed to go, the correct formatting will be maintained.