http://www.altera.com/literature/ug/ug_embedded_ip.pdf Chapter 28 "Interval Timer Core"
This describes an off-the-shelf timer and from reading the functional description you can get an idea of what is involved. But the bottom line is that it is basically just a counter possibly with a comparison against a programmed value.
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From my understanding Im going to have to use the system clock and and divide it out to a Hz that will benefit me.
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That is more like what you would do with a microprocessor/microcontroller and software: you would program the timer hardware to generate an interrupt at a given frequency (1KHz?) and then write software ISR to manage possibly many software timers (counters) and generate software events when they have expired.
There is nothing stopping you from following that approach, but unless you are short on resources, there is no need for that complication and all of your timers can operate directly from the system clock.