Im pretty sure this is a very simple question and it can be solved pretty simple but i installed some modifications on my forum and they seem to be able to run with the default forum theme but when i change themes and use a theme i downloaded the mods wont appear..I know i will probably have to mess with the coding or something..But where?Thanks
You only waited 4 hours before bumping your own thread? You should wait at least one business day.
Your question is very generic.
I can only answer: you should edit the custom template, but as we don't know what plugins have this problem, we should investigate in the code for finding the place in which edit.
My suggestion is to contact the plugin's developer for fixing this bug with custom templates.
Most plugins which perform template edits are somewhat delicate, as they try to find where to insert their code, however, not all themes have ideal templates (to the plugin) so the plugin may fall over when trying to do the replacement.
The other common thing is that installing themes after plugins, the themes can override some templates customized by plugins.