If you're using Cubase SX it's easy to automate. Bring up the mixer, hit the W on the channel you've got the filter effect on, hit play and then tweak the filter in real-time. The W stands for write, and when you hit stop SX will have recorded all the real-time filter movement you made. After that, make sure the R button (next to the W one) is green (i.e. the automation data is being read) and you're sorted.