So, I want to fill a glass with water/fluid, but I want to do from the bottom and am running into some issues.

When the source is covered, it stops filling. I've been told to use divergence, which does seem to work in principle, but it also causes all of the fluid to rise/expand, which i dont want, just want it to happen at the source.

So what is the best way to do this? (using dopnet)

Here is a basic setup for using divergence.

When the source is covered it will stop filling without divergence (normal behavior), with divergence
the fluid will continue to rise unless stopped by clipping/removing etc (normal behavior)

Not sure what you mean by "which I don't want, just want it to happen at the source."

Maybe this helps you.