Ok, here's some tips about things you asked and some things I wish I knew when I started.
Based solely on my own experience using tmo (and this will vary from mod to mod), I would call *safe* srufaced distance at about 6 miles during daylight and 5,000 yards at night. You can get closer depending on aspect ratio (if the target is at bearing 0, you have a much smaller profile than if the target is at bearing 90), speed, visibility conditions, etc.
You talk alot about passive sonar. I have done quite a bit of practice with it and don't recommend it in general as the result is quite inaccurate. The other big reason I don't reccomend passive sonar only plots involves the fact that it requires a course/speed change when the target starts to get close. The more radical the change, the better for accuracy. In my experience, the US fleetboats, with their poor turn rates when moving silently, this generally requires engines at ahead 2/3 minimum to make a time deadline. Combine this with the fact that japanese merchants have hydrophone sets, and this often means that the merchant is alerted to your presence and begins evasive action, spoiling your plot and your shot.
Unless visibility is horrible, you are better off getting a visual range estimate using the stadimeter. You didn't mention this tool anywhere, so I suggest you look into what it is if you don't already know.
Personally, I would say that accurate stadimeter readings are limited to about 4,000 yards with good visibility.
I did write something a while back about accurate estimation of target range at very long ranges. In that case, I got an accurate reading on at target that was 11,000 yards away. It can be found here:
http://www.subsim.com/radioroom/showthread.php?t=201121
One technique that will help you close in on a target that you are ahead of to attack position is the simple collision course technique. There is a concept called "constant bearing decreasing range", which exactly describes a collision course. It's easiest to describe this by example.
So suppose that there is a merchant to the northwest heading towards your position and you are submerged ahead of him off of his port bow. His general course means that you need to head west. Turn to heading 270 and point your periscope right at him and don't move it. If the target is moving from right to left, he will reach the point of collision before you do and you need to turn left more or increase speed. If the target is moving from left to right, he will reach the point of collision after you do so turn right more or decrease speed. It will probably take you a few tries to get it right. Obviously, you don't want to actually collide with him, so at some point you will need to either turn into him or slow down.
You asked about striking more than one ship in a single attack and I was already thinking about putting a tutorial up. I'll probably put something up about it in the next couple of days. I don't really recommend the practice until you hit a point in the war where your torpedoes are fairly reliable though. Before that point, I'm usually firing 4 torpedoes at any good size target and usually 3 at smaller targets just to try to ensure that at least one of them works. Later in the war, I tend to fire between 1 and 3 depending on target size.
When identifying ships, look for distinguishing features. For example, if the smokestack is in the back on the ship instead of the middle, it is a tanker. Pay attention to the way the central part of the ship, the masts, the smokestack, etc is configured. Be on the lookout for distinctive setups in the gunwale, etc. In time, you will probably memorize a good portion of the ships in the game. There's a few I still get mixed up (momoyama maru and ryuun maru ever frickin time), but mostly I can id every merchantman in the game at a glance now. Noteworthy is the fact that it is a *lot* easier to identify a ship from the side than it is from the bow. In the radar era, when I'm usually in attack position well before I can even see the ships, I often don't even identify until just before I fire.