Annotate Reference Designators from a Text File

One method is to use Schematic Editor > Tools > Annotate > Back Annotate Schematics and load in a Was-Is file. The Was-Is file is simply a text file with the current designator a space (not tabs) and the new designator on each line.

C1 C4
C2 C3
C3 C2
C4 C1

The file name has a .was extension.
This will change both the schematic and the PCB designators, not just the PCB designators.
Copy / pasting from Excel to a text editor works but you will have to change all the delimiters from tabs to spaces. 

If you want to change only the PCB side then paste into the string column of the designators in the PCB List panel and re-link components by designator should work.

Source: 

Annotate Reference Designators from a text file? - Altium Discussion Forums - Eric Albach

That's it ! 

NetTies and PAD Classes

Pad Class can be used to suppress Net Tie Hole to Hole Violations.

As shown below two multilayer pads were place on top of each other to create Net Ties that can be used to connect tracks or copper on any layers.

Design > Classes > Pad Class > NetTie PADs

Design > Rules > HoleToHoleClearanceNetTies

That's it !