I haven't touched Fritzing in at least 6 months, so I don't recall if it has this feature...
But in Eagle (and other schematic capture tools), you can just attach a wire to the pins of a schematic symbol, without routing them on the drawing surface. In the schematic diagram, it looks like a short wire that goes from the microcontroller lead to nowhere. This wire is generally referred to as a "net". And if you give more than one of these "net" wires the same name, the software will recognize that they are really connected together once you go to the board layout part of the tool. In other words, if you have a short wire named "VCC" in one part of your schematic, then the software will behave as though you had wiring drawn to connect it to all other wires named "VCC".
For example, many components will have a connection to ground. All of your microcontroller sockets will have at least one (and the middle one that can accept two chips will have two grounded pins). If you simply connect all of those pins with wires on your schematic, it will look like a mess of spaghetti. But instead of connecting them all with routed wires, just attach a short wire to each one, and give them all the same name ("GND" for example). This is electrically exactly the same thing, but without the clutter in your diagram. Once you switch over to board layout to figure out how to place everything and where to solder physical wires, it will want to physically connect all nets which share the same name together.
So for an AVR programmer, you would essentially just drop the appropriate chips into the schematic. Then attach small wire nets to each of the programming pins (gnd, vcc, miso, mosi, sck, rst), naming them accordingly. This will give you exactly the same circuit model, without any of the spaghetti wire routing on the schematic.
Don't go overboard with it though. Small IC's or discrete components should be wired together with connecting wires so that the circuit can be easily understood. Only use the named nets trick when you need to break the schematic up into logical sections or when there is complex routing between IC's like in this case.