Under project options you can modify the physical component names by going to the Multi-Channel Tab.
Typically in large multichannel projects you append numbers to signify the channel offset and then the actual logical designator.
For example:
You have 2 sheets that you use 2 and 3 times respectively. Lets call the first Circuit 1 and the second Circuit 2.
When you go to annotate your design you assign the starting designator of each sheet
for circuit 1 you set it to 100 and for circuit 2 you set it to 200
On Circuit 1 you have a designator like R101, and C110
On Circuit 2 you have a designator like R205, and C202
Now when you go to compile to physical designators you tell it to do the following
$ComponentPrefix$ChannelIndex$ComponentIndex
And the physical designators for the above components turn into:
RX101 and CX110 Where x is the channel index of circuit 1
RY205 and CY202 Where y is the channel index of circuit 2
Since circuit 1 is used 2 times the designators you get
R1101, R2101, C1110, C2110
If you would rather not deal with annotating like this, you can do a board level annotation to make the designators all flat no matter how they were compiled.
**Update**
Another thing to note is that when you go to generate a pdf of your schematic, make sure you are referencing the physical documents if you want to see the whole schematic.