First I have to chime in with rama:
Using ISO files on HDD is definitely the best way to run PS2 games, for many reasons. I do this even when running games on my PS2 consoles, using OPL (Open PS2 Loader) to load those games over LAN from an HDD of one of my computers. (It's the same ISO collection I use with PCSX2

)
But your original question also deserves an answer:
(10-07-2012, 10:42 PM)blitches Wrote: I dont consider that much of a noob with emulators, but this is my first time using pcsx2, i have everything set up, everything is running fine, but my question is how do i make my copied games run smoother? when i put a real game in, it works perfectly, but when i put a burned game in, the frame rate dips to about 15-20 when gameplay starts.
This obviously means that the burned discs are being read slower than the original game discs. That is very common, and is usually due to one or both of two specific reasons.
1: Cheap discs often have low speed capacity, though fake brands often mark them as being of a high speed type. But they can still only be read reliably at the rate they were really designed for (if even that). Fake marking also contributes to instances of #2 below.
2: Disc burn speed affects readability, in ways that some people misunderstand. One common myth is that the slowest speed is necessarily best, while another myth is that it's best to burn at the max available speed. Both myths are equally false. A burnable disc was designed to let a focused energy beam induce a photochemical reaction in the photosensitive layer. There is not only a top speed for this process to be reliable, but also a bottom speed, and optimum speed is somewhere in the middle between these two. That is the burn speed for which you can expect best read performance, leading to a minimum of misreads (which could cause retry delays).
Best regards: dlanor