is there a way to install updates and patches online into a running QNX 6 system?


There used to be one, but in the latest version of the OS it`s gone.

If you mean a “standard patch” from QNX (that is, a tar file with shiplist and manifest files, and host and/or target directories), there’s an applypatch utility that’s included in QNX SDP 6.4.1. You can also get it (as a patch!) to install on 6.4.0. On earlier releases, you have to follow the instructions in the patch’s installation note.