Since I'm playing a lot on my notebook I'm sometimes forced (by various circumstances) to play on the touchpad. While it is definitely possible and not as a pain as it might seem, it is a bit harder than using the mouse. I found out that with some practice I was able to play against Hard AI quite well (won most of the time) and even the campaign is playable (most missions on Medium though, many Hard achievements are much harder to get when using the touchpad).
The key to success is to use the keyboard as much as possible. Everything should be mapped to a group - units, workers, production buildings. Use space to get to the action immediately when something happens. With some training, you should be ok. I wouldn't however attempt to play against people in 1v1 Quickmatch, especially if you are ranked gold or higher.
The most important thing to realize is that 3 workers per mineral is the max you would want. It is not necessarily optimal however. The third worker is not as effective as the first 2. Once you have more than 2 workers, one of them will always be "hanging around" waiting for its turn to be useful. Therefore, if you have an expo with less than 2 workers per patch, you would do better to move some workers there. You will get more minerals per minute by having 2 workers per patch at your main and 1 per patch at your expo than you would with 3 workers per patch at your main.
With that in mind, here are some answers:
How to keep track of how many you have at a specific base?
Make sure all your mineral patches and gas geysers are visible on the screen. Now double click on one of your workers. This will select all your workers. At the bottom middle of your screen you'll see wireframes of all of them, 8 per row. if you have 3 rows full, that's 24 workers, which is a decently saturated base. "Full" saturation would be about 24 on minerals and 6 on gas, or 30. But if you have an expo, you're better off moving some of them... (Note that MULEs do not conflict with SCV's for mining time, so they should not factor into your counts.)
When you expand, should you build workers from that base or transfer?
This depends on the situation. If your expo is far away from your main, and there are potentially enemy forces in between, then transferring is probably a bad idea. If you have more than 2 workers per patch in your main, and your natural is nearby and well defended, then transferring makes sense. In my experience, Zerg players usually expand before they have much more than 2 workers per patch, while a 1 base terran or protoss will often build up 30 workers on one base before expanding.
**Rebuilding after some being killed **
I'm not sure what the question is here - you can just rebuild them like you normally build them.
Transferring when minerals run out
There is no automatic way to have workers move to an expansion when minerals or gas run out. However, you can listen for the voice that says "mineral patch depleted" and start transferring them. You can also look for the idle worker icon that pops up on the lower left hand side of your screen, that will alert you to a worker who is not doing anything.
Race Specific Tidbits
Protoss can chronoboost workers to help get an economy up and running, or recover from an attack.
Terrans can get by with less SCVs if they have a lot of orbital commands to summon MULEs with.
Terrans can load SCV's into command centers, then fly them to a new base.
Zerg players need to remember to build more drones to replace drones used to build buildings.
Best Answer
As JavadocMD pointed we have discussed Queen usage at length. To help extrapolate on the Queen consider the following: If you have 3 or more Hatcheries, its likely that you're approaching the Control cap. At this point is it really worth it to produce additional Queens which will not be involved in battle? The Queen does work as an efficient defensive unit, but Spine/Spore Crawlers can also function in this roll and require no additional Supply. Additionally, if you have more than 3 Hatcheries, your production is very high, and as those bases become mined out, your income will not be as high. Thus its often less worthwhile to produce Queens at bases after your first expansion or two.
On the subject of Chrono Boost, I often find it hard to spend efficiently late game but here are a couple things that may help:
For what its worth, I still have the habit of cycling through my Hatcheries every ~25 seconds to guarantee effective usage. Because of smart cast I can even leave all my queens in one group if necessary.