I'm a bit behind with the story of my son's train set, so let me finish the tale of track-laying. Of course it wasn't long after half-term I was being pestered to create the upper station.
These are the tools I use: pliers and small hammer for the pins, the end-cutters and screwdriver are useful for levering out pins when required. The scalpel is for trimming sleepers and slicing off the "chairs" to let the rail joiners fit. The orange-handled cutters on the left are Xuron track cutters, for years I used a slitting disk in a mini-drill which is certainly effective but the trac cutters are quicker and quieter. A fine file is used to clean up the rail end.
Talking of track pins, here's a comparison. At the centre are PECO pins, long and thin and frankly useless. They only really work with "Sundeala board" which is basically compressed paper, sags, disintegrates, and is generally useless as a baseboard top. Even then you need to drill the sleepers with a 0.5mm bit - never mind tedious you'll be forever breaking bits too! If you use set-track you'll find the pre-drilled holes too big. Also they often protrude through the baseboard, ready to slice fingers and knuckles! The bent pin tells it all - these area fast route to frustration.
So for years I've preferred Hornby pins (top left), these are strong enough to be hammered into most baseboard surfaces (including ply) without a pre-drilled hole, and are a tight fit in set-track pin holes. They will go through a sleeper too, though pre-drilling is probably a better idea I rarely bother. The head is bigger and more visible, but when laying track on a "serious" layout I glue it, adding pins around the rails and sleepers to hold it, and pull them out afterwards. So many of these Hornby pins have been used several times already!
When I was running low I popped into Gaugemaster (fortuitously quite local to us) to get more Hornby pins, but saw that Gaugemaster sell their own variant (GM66 if you are interested). These are very similar to the Hornby ones but with a flatter head, and you get more in a pack for similar money. They do a "PECO" style of pin too, but these shorter ones are the ones I'd recommend!
Anyway here's the finished track layout, with platforms being fitted for the upper station. The next task was to wire it all up!