Here is the PolyEd How To Guide on making a level.
Basically I will put a few points in to get you started;  look at the mapspecs.htm file for details on using the spawnflags and platform making, etc.  My thanks and appologies to Niklata, Oliver Montunay, and the others.

Note that in the specs you might see stuff like:
"open_once"
"1st_left"
"1st_down"
"no_shoot"
"always_shoot"
under key names for a func_door_secret.
anytime you see these keynames that don't have any matching values, interpret it like this:
the first keyname means add 1 to the spawnflags argument:
for "open_once" add 1 to spawnflags.
for "1st_left" add 2 to spawnflags.
for "1st_down" add 4 to spawnflags.
for "no_shoot" add 8 to spawnflags.
and for "always_shoot" add 16 to spawnflags.
Note how the number to add doubles as you go down the list.


First, you need a texture wad.  Download quaketex.zip with the quake101.wad.  This wad will have every texture from Quake version 1.01.  Hopefully it will be included in any CD you find with PolyEd on it.

Second, get Qbsp, Light, & Vis stuff.  They will all be in a qbsp package...  try cdrom.com in the qbsp_pak_tools section.  Get the ones for registerd version, and get either the DOS or the windows ones.  Make sure they are for the registered version.

Make a map, f3 to save a map file, and then at a dos prompt do this:
qbsp mymap  {this will build it}
light mymap {this will put the proper light sources in the right places}
vis mymap {this will optomize kind of}

then copy the resulting bsp file to your id1/maps directory.  What?  you don't have a maps directory?  Well just make one.  Now go into quake, pull down the console and type: map mymap.  

if your level wont vis it has leaks.  to determine where leaks are copy the mymap.pts file to your id1/maps directory.  when playing your level bring down the console and type: pointfile.  This should put a stream of grey light around areas of leakage...  Just noclip around and find some corners that don't come together enough.  Sometimes they may be in the same spot when you're editing in polyed, but qbsp doesn't always put them together right...  (this is sometimes your fault as well if the face points aren't all aligned in a flat plane; poled will let you put face corners in places that will give you a bent plane, but it will only give qbsp 3 corners, and qbsp will determine where the plane crosses other planes.)  Sometimes you just have leaks where you shouldn't; in that case, just bring the walls together more so they actually share the same space at the corners.

Notes on map making:
This is not like doom.  You arn't building sectors, you're putting walls together, walls that have thickness.  Think of it as big slabs.  And remember, 4 walls are not enough to make a room, You must not forget to put a cieling and a floor in.

the mapspecs.htm file will guide you in making those flickering lights and teleport devices and all the other cool stuff.