Hi Stacey, I just got back from Madrid and I loved El Escorial so much that I went back a second time. The first time I was so thrilled to be surrounded by a mountain on one side and a valley on the other, with clean air in between, that I didn't even bother going into the monastery. Just walking the charming little streets, enjoying a long lunch, sitting at the monastery gardens ... was enough. (It's free to stroll around in the garden.) The second time, I did the official guided tour of the place, which was pretty good. Since you don't have a lot of time, here are some suggestions.
The cercanías train takes you there in 45 minutes from Atocha (shorter if you start at Nuevos Ministerios or Chamartin). It is a lovely, relaxing train ride, from which you will enjoy even lovelier views (there's a park full of deer on the way). Once at the El Escorial, take the "circular" bus to the town, which is called San Lorenzo del Escorial. (Otherwise it's a 2km uphill walk!) Head left from the bus station and eventually you'll end up at the monastery.
The tourism office is just to the right of the monastery's main entrance.
If you get up early and get on that train you can definitely enjoy El Escorial without giving up Madrid in the evening. I think the first train leaves very early ... you can easily make it there by 9 AM and be back in Madrid by 6 PM. The schedules are clearly posted in all the train stations. Ask the clerk for a fold out schedule. You will need it to check times. Trains from El Escorial run about one an hour.
As for Toledo, it's much bigger and if you have a chance, see the sites in the afternoon and stay for the evening. It's a tad bit too much like Disneyworld now during the day ... I don't mean the place itself, of course, but the number of tourists and souvenir shops are really distracting (and yes, one is always part of the "problem.")
The train also takes you to Toledo in about the same amount of time. It is a "regionales" train and very comfortable. You also need to take a bus or taxi to city center.
I would skip the bus tours if you can. It's cheaper and more fun to do it on your own. All you need is a map (go to the tourism offices first) and a lot of energy to explore!
Have a great time!
Churrito
PS There is a plaza to the right of the monastery with a restaurant called El Candil. Great vegetable soup ("meneste de verduras.")
Oh also, the monastery cafeteria makes GREAT croquetas, and you can order them by the piece!!! Enjoy a couple with a beer while you're waiting for the guide to group everyone.