Is it better to spread out the satellites or concentrate them in one area

The following correct information to the best of my knowledge, but is generally based on my own gameplay experience and memory, and not backed with SCIENCE (TM). I'm happy to correct any errors noted in comments.

General Line of Sight and Cover

This Image (it's large) provides a great guide to cover and it's effects on line of sight(LOS). I found it via reddit, but I'm not sure of it's original source.

Based on my experience, low cover doesn't block line of sight, and high cover does block line of sight. However, it's important to note that if your unit is peeking around the edge of a piece of high cover, the enemy can see them peeking out, and can still establish a line of sight, even though most of your unit is behind high cover.

When thinking about cover and line of sight, it's important to consider that your soldiers are "active" at all times, looking over their shoulders, peeking out from cover, sometimes even automatically sidestepping a space to take a better shot. Being active in such a way allows your units to maintain a 360 degree line of sight, but also exposes them to enemy fire. Your unit may be in cover, but they're peeking out from it constantly to maintain line of sight on the enemy, and that gives the enemy a line of sight on your soldier.

A good rule of thumb is, if you can see your enemy, there's some kind of line of sight between him and you. If you're being shot at from within the fog of war, then I'm not sure what's going on there. I've only seen that happen when I'm hunkered down (which reduces a unit's line of sight).

Unfortunately, when all your soldiers are bunched together, it's hard to know which particular soldier is giving you visibility on any particular square. The game doesn't provide any way to determine a soldier's individual LOS when multiple soldiers have overlapping fields of view.

The Hill Scenario

For the "Hill Scenario" you described, here's what I'm imagining (side view from ground)

        __+__
  _____|FFFFF|_____
S|HHHHHHHHHHHHHHHHH|X

H: Hill (terrain)
F: Fountain (cover object)
S: Soldier
X: X-Ray

Let's assume that the fountain is a half-cover object for now. In the above section, we assume that half-cover doesn't affect line of sight. This should always be true on flat ground. However, in three dimensions, the relevant question seems to be, "if the terrain is a half-step up, and the fountain is a piece of half-cover, shouldn't that equal full cover, and block line of sight?" The image I linked to above does not address this scenario.

Realistically, line of sight should probably be blocked in this scenario. However, you got shot, so it obviously wasn't.

I'd theorize that the game simply treats low cover objects as not blocking line of sight, and doesn't actually calculate total "height" of cover.

If this is the case, we can completely disregard the fountain (pretend it's invisible and immaterial). This means that the elevation of the Hill would be the key to determining LOS.

If the side of the hill is the height of low cover, then there would still be line of sight across the hill, when ignoring the fountain.

If the hill is the height of full cover, then I feel like it should block line of sight, and this is probably a bug. I could see a possible argument that the soldier could be actively peeking his head out over the hill, creating a LOS across the hill. However, based on the unit height and animations of the soldiers, it seems like it would be very difficult for one of them to fire over a piece of high cover.

If the hill is higher than a full-cover object, then there should definitely be no line of sight across the hill, even ignoring the fountain.

If the fountain is full-height cover, then it should block LOS between the two units regardless of the hill height.

I would recommend dedicated the entire right side of your base to laboratories and workshops, save for 1 or 2 rooms, which you will need for facilities that get no adjacency bonuses.

You will need to build 6 facilities that get no adjacency bonuses (Officer Training, Alien Containment, Foundry, Psionic Labs and 2 plot facilities which cannot later be removed or moved), and 2 square blocks of 4: 2 Satellite Uplink + 2 Satellite Nexus for a total of 16 satellites (which is exactly the number of satellites you need) + 2 Power Generator + Steam Generator + Elerium Generator to power the whole thing (a base with such a layout will produce 107 power and draw 102 power; you can replace the Thermo Generator with an Elerium generator if no steam block is in a suitable location, allowing you to drop 1 Power Generator and placing one of the non-adjacent facilities there, freeing up a slot in the right wing for another lab/workshop).

As you can see, 6 + 2 * 4 = 14, the number of rooms in one side of your base + 2. The 2 extra facilities will overflow into the right corner of the base, as so:

You can shuffle the blocks around, what's important is that you don't put facilities that get no adjacency bonuses in such a place that it will block bonuses for facilities that do

Should you ever become rich like Scrooge, you can remove 1 Power and 1 Thermo Generators and build a second Elerium Generator, allowing you to move 1 facility that get no adjacency bonuses from the right side to the left side.

Note that the laboratories have been replaced with workshops - by this point you will likely have researched everything there is to research. You may also wish to demolish Alien Containment after interrogating every type of enemy, as doing so will turn surplus live aliens into useful corpses, allowing you to stun aliens for their enemies without sacrificing the body count, as well as free up a slot for a facility that doesn't have adjacency bonuses.

Proof of concept screenshot. Note my improper placement of plot facility 2 - it should be in a corner. Also note how blocks have been shuffled around to accommodate various demands over the base's lifetime.

Enemy Within addendum

The expansion introduces some new factors, but the situation remains largely unchanged: The Genetics Lab counts as a laboratory and the Cybernetics Lab counts as a workshop for adjacency bonuses, so you can build them as you would build laboratories and workshops above (make sure to fit the Gene lab in a corner if you're going to replace the laboratories with workshops later). The foundry has also been given workshop adjacency bonuses, so you can move it out of the laboratory block to the workshop block for some increased efficiency.