When Quartus compiles a project it does several things. The first is to look through all the HDL source code that you wrote or that was generated by the SOPC builder and extract the Hierarchy for your design. In other words it's discovering what design entities are used in your design and what source code files they are located in.
It then synthesizes the source code meaning it compiles it to a netlist of primitive gates.
The fitter takes this netlist and decides where everything should be placed physically inside the FPGA. This is where the timing comes in. Suppose there are two registers in your design somewhere. They run at a 10ns clock (100MHz) and the one register latches the output data from the other register. Well if the fitter places these two registers too far apart from each other, then it may take longer than 10ns for the output data of the one register to reach the input of the other register. This is a timing violation and the timing analyzer will report this at the end of compilation.
Now fixing these problems is another issue. I'm going to assume that you're having trouble meeting timing on something that SOPC builder generated and not your own HDL code. If it were your code then you would want to look at the violated timing paths and change your HDL code to improve timing. However, tweaking your SOPC system can have a huge impact on your timing. But if you simply can't tweak your system then we'll instead look at some of the fitter options that you can set to help the fitter make timing.
One thing you could do is run the timing optimization advisor. I think in Quartus 5.1 it was located under the tools menu. I'm using Quartus 6.0 now so I don't remember. This will kind of guide you through things you can do to improve timing. However, a lot of its recommendations will cause your compile time to skyrocket. If you don't want to run the timing advisor then you can try tweaking some settings on your own. In Quartus, click on the Assignments->Settings menu. Then in the left pane click on the Fitter Settings. Here is where you can change some of the fitter options. Click on the More Settings button to find even more options.
This post has gotten long so you'll have to take it from here. If you have more specific questions, feel free to post them. It's very difficult to cover the topic of making timing in a forum post. That's what Electrical Engineers get paid to do.