As you have already recognized it is not a problem of uddeIM itself.

In most cases the site template or a module uses the same resources as uddeIM uses, e.g. uddeIM notifier requires the "onload" handler and timers. When the template or another modules overwrites these uddeIM cannot work.

There is no solution for that except you do some coding. E.g. when the onload handler is overwritten by two modules, create an own function that is called by the onload handler and call both modules from this function.

Building Joomla sites (or other CMS based sites) is not that easy as lots of people think (just installing some modules and components) you have to be familiar with html, css, php, mysql, javascript and some other techniques, except for very simple sites.