mikroC's debugger is just an "Instruction Set Simulator". That's why it can execute the individual instructions of PIC core but it has no understanding of PIC's peripherals like the Timer you are trying to simulate.
Better use MPLAB or ISIS or even better switch to some other sensible compiler such as cc5x/hi-tech/iar
But AFAIK mikroC doesn't output cod/coff/elf or any other files that can be loaded into ISIS or MPLAB. If I remember correctly there was a tool that can convert mikroC files to coff. Search forum or net, you'll get it, but don't how much it works
Hope that helps,