Please answer following so that we can help you out..
1. Which Operating System are you on.
2. Which version of Reader or Acrobat are you using.
3. What is the error / warning you get when you carry on with your workflows.
4. What exactly are you unable to do : open a specific PDF , Open PDF's locally , Open Pdf's online
Ideally installation of Reader should not affect activities which do not involve Reader. Say opening internet explorer for general browsing or using your email client .