[Black Tiger]

1.) I'm not sure about that, but if it's not unique, just paste more code in the "search for" window (the upper window) so that it -is- unique. If done that way, you are always sure it only changes the one thing you want changed.

2.) vB upgrade will change nothing of your TMS system. If a template get changed by vBulletin this is what happens:
a.) You upgrade your vbulletin
b.) You login to your admincp
c.) TMS system will doe a check automatically or at least if you refresh your screen once. Then it will see things are changed, you get a list of OK templates which you changed in TMS, but the templates which are change by vBulletin will get a sign that it's not oke, you will get notified.
d.) You check the original vB template for the changed code and change the changed code in your TMS system.
e.) Rerun the template check from TMS and all will be fine.