How to oerform a functional simulation of a QuartusII design with Modelsim?

Hi All,
we are having troubles in simulating our design with QuartusII.
We found that the QuartusII simulator is dramatically slow since every
time we must perform the whole compilation procedure before simulating,
even if we'd like to perform a functional (not timing) simulation; so
we are now trying to use Modelsim.
We set the QuartusII to launch Modelsim (through the NativeLink
feature); by the way, compilation seems to be necessary in any case,
and the problem is that Quartus, while optimizing the design,
eliminates some signals that instead could be useful to simulation.
We tried to create a project from scratch with Modelsim and include all
our source files, in order to simulate the whole design without
starting the Quartus environment, but since we are using schematics and
Altera MegaFunction blocks (LMP_RAM_DP, PLLs, etc.) it turned out to be
a bit complicated to set up the Modelsim project and keep it up-to-date
with the Quartus project.

Have you encounted the same problems with Modelsim+Quartus?
Can anyone suggest us a better way of proceeding?
Referring to our experience, from the Xilinx ISE we were able to launch
the Modelsim simulation very easily, and we could also simulate
separately each single module of a design...

Thank you in advance.