I too recently took the plunge into hand laying track, and I'm convinced it's a worthwhile endeavor whether or not you choose to stick with hand laying or flex track/premade. Here's what I learned.Mike Tylick wrote a great article about hand laying switches on his F&S Junction module. This has been the method I've used and loved.
Tony Koester also wrote an article for MR about laying switches. This article as well as the one above (I think) are reprinted in a new book from Kalmbach on Track and Lineside Details, etc. (not the actual title, but something like that.)
I highly recommend getting at least two of the 3-point guages. Mine are from Kadee - code 70 on one side, code 100 on the other.
The other posts seem to cover the basics fine enough; glue ties, sand, stain, balast then rail. Just go the extra step and paint the rail and distress the ties. I seem to remember an article in MR not too long ago about how George Sellios does this on the F&SM.
A good source for ties, rail, spikes, and even advice if you ask is Blackstone Valley Railway. Good bridge & trestle kits too, BTW. www.blackstonevalleyry.com Right now production is suspended on the kits, but you may still be able to get rail, ties, etc.
Building a small switching shelf railway, I was able to use yardsticks (free from many hardware stores) as a subroadbed. As long as the spikes are short enough to stay in the ties, you're good.
Oh, When you lay a switch, plan ahead about how you intend to wire the frog and the points. If you're using an expensive motor drive this may not be a problem as these usually include extra terminals for wiring the frog, signals, etc. I came up with my own method for using a Caboose ground throw (N-scale rigid) and an SPST micro switch. In the future I'll be trying another method. Not that this one was bad, but troublesome to install under the points. Tylick offers a method in his article.
Good luck and remember; measure ten, cut one.