First question: There's a certain acronym I could use here, but I won't. Suffice it to say, if you'd followed the directions in the readme, the active topics link would still be there.
Second question: What you do with other hacks is your business. CH2 and it's XHTML base make major changes to every public template file, and as such it is not particularly friendly with the point-and-click, instant gratification hacking style most people use. If you want it to cooperate with your other hacks, it's up to you to make it work.
---Jamin