1) Each hole is independent of the others. This is what you linked. However you can easily use solder bridge to adjacent pads or the ground plane, either intentionally or unintentionally.
I have a problem getting them to bridge intentionally, but I have round solder pads -- the SparkFun square pads should be much better. For round pads, the solder likes to ball up on each pad and doesn't like to spill over to it's neighbor. But, my soldering iron is not temperature controlled so I might be getting things too hot. And I'm using flux-core solder, maybe flux-free solder would help in this situation.
I'm not a fan of bread-board style protoboard. Yeah you can copy your breadboard layout straight over, but breadboard layout is messy! It takes up a lot of space too. Perfboard is much more compact and ends up being neater because of it.
One thing I like to do with perfboard is lay a piece of straight (stretch it to make it perfectly straight) bare solid wire along an entire row on the bottom pad / solder side, and tack it to single pads at both ends to make a ground or VCC "bus". Then I can just tap in to the bus anywhere convenient with a component through a hole on the bus row. Much less hassle than making big long strings of solder bridges and less likely to toast components with the excessive heat that requires. Aligning the bus with an Atmega328's PDIP VCC/GND pins is convenient, except the bus has to cross over itself under the chip (WHY Atmel?! Why did you do that!?). I use insulated wire for the crossover, obviously.
On the top / component side, pieces of wire taken from Cat5 Ethernet cable are cheap and work well to connect distant components. Leave the insulation a little long as it shrinks when heated during soldering.