Good Question !! I have tried it, both type of channels can be used on same page, BUT (A big BUT) report become ambiguous.
As far as I know there shouldn't be any problems (and I have noticed none), especially as both serve a quite diferent purpose: Custom channels to track individual ad units and Url channels to track whole websites.
You can use it, but then your channel data will overlap. For example: You set up a url channel for page1.html Page1.html contains two ad units with custom channels each - AdTop and AdBottom. Now at the end of the day, your channel data will show URL earnings (consisting of both AdTop and AdBottom) + AdTop earnings + AdBottom earnings. That will make it appear as if you have earned double the revenue, which is not the case.
Is it advantage for having the same channel for one site vs. multiple channels (ad units, normal ad, etc) for the same site?
I have created both custon channels and url channels... however, I have often wondered if creating channels impacts on CTR or CPM... or does it only offer information...
Yes and No. Creating custom channels do not directly increases CTR or eCPM. However monitoring the CTR and eCPM of each adunits and than changing the location and keywords according to the report, you can make a big difference. So keep on creating channels and monitoring the results and than optimizing them.