Oy vey... How about the moon from the sky while I'm at it

First things first... RTFM, especially the FMC chapter, the docs are your best friend with the PMDG...
EDIT: Since I have been reading "official" FMC documentation and using the Project Magenta glass cockpit software, I have gotten used to using "official" abbreviations for stuff to do with the 737 cockpit. If any of what follows doesn't make sense, just ask and I'll write up a quick glossary of terms...[/i]
FURTHER EDIT: and of course I am assuming you want to do full-on CAT IIIA (FMC pretty much the whole way) here.[/i]
To be honest, I don't use FSNav as more than a moving map any more (even when I'm flying tours...). Entering the route directly into the FMC (Project Magenta in my case, but the PMDG one is almost as good...) is by far the easiest way to do such things, especially if you want the FMC to do all the hard work, as it [the FMC] leads you logically through the pre-departure programming.
Any how, as far as getting the climb and cruise alt right, you'd normally set these after entering the route - basic programming order from "cold" is POS INIT, ROUTE, DEP/APP, PERF INIT and LIMIT - the important pages are PERF INIT and LIMIT...
PERF INIT is where you specify the cost index (which despite what I have read elsewhere the PMDG FMC does take note of, enter CI of 500 and the autothrottle will do it's damnedest to get you to your destination in the shortest amount of time!) and cruise alt (TRIP/CRZ ALT by LSK1R, the value on the left is the calculated ECON cruise)
LIMIT (and there are three or four separate page groups for this) is where you specify things like flap setting for takeoff, climb profiles, N1 limits, and calculate the V-refs and so on.
Any time you see square boxes in the FMC, it is expecting an input from you (as the pilot). As mentioned above, the docs tell you all this...
Finally, once you've got a fully programmed FMC, set the MCP (autopilot) for takeoff - HDG should be runway heading, ALT is your initial alt (as given by ATC) or cruise alt if you've not been given an initial alt. Turn on the F/D, arm the autothrottle, and when you get take-off clearance, turn on TOGA (top left screw on the MCP) and when you hear "rotate" pull back on the control column and hand fly to your first waypoint (you can enable VNAV during the climb out). Once you are close to your first waypoint, enable LNAV and CMD A and let the computer take over...
And regarding FMC DES, you must have entered the altitude you want to descend to long before you get to the computed T/D.