kicadschematics
I'm a bit confused about where I need to place a junction on the schematic, and where I don't. For example:
My schematic is below. I've just let KiCad do the work for me, but I'm not really sure if my wires are really being connected as they should. I currently only have one junction – attached to pin 19.
I generally want signals to flow from left to right, so I put inputs on the left of the box, and outputs on the right. Power connections (if shown) go on top, and power (again, if shown) on the bottom edge. The box must, of course, be tall enough to show all the pins, but only needs to be wide enought that the pin names don't overlap. I would usually put the reference designator and part type above the part, not inside it.
Spacing of pin/signal groups, as in your right example, can be helpful in separating functions on a part.
You can do this without a schematic. Open PcbNew and click on 
at the right hand side. This will allow you to add any footprint, such as a 1x1 pin header. Make sure your grid is 100 mil. As a proof of concept, I used the 1x5 pin headers 
.
Best Answer
Usually you have to place a junction wherever two wires that should be connected are crossing each other. In the situations you mentioned, the connection should be made automatically by the software. Also if you draw a wire that ends on or starts from another wire it should get connected automatically.
If you're not sure that the pins or wires are connected you should use the Electrical Rule Check function.