Something you don't want to do, though, nathanas, is make this a "habit". The reason being that the socket that is on the Arduino board is not designed for repeated insertions and extractions; over time you will wear it out, and contact will become intermittent.
If you absolutely need to do this, there are some options:
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Switch to bare-bones ICSP programming (will require some investment in hardware, time to learn the process, and a minor update to the Arduino configuration), and put a header for it on your standalone PCB.
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Continue to use a bootloaded ATMega in your projects, but use an FTDI cable or breakout board and put a header on your standalone PCB for this purpose.
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Build a ZIF (zero-insertion force) socket interface for the ATMega, either separate from the Arduino board, or as a shield (I've posted before how this might be possible using a prototyping shield, and I think there may be manufactured versions for sale - I also know of an example floating around the arduino.cc website, maybe in the playground somewhere).
One other thing, if you haven't already experienced it: When inserting a new IC into a socket, you may find that the pins of the IC are spread "wide" and the IC doesn't want to "seat" into the socket. Sometimes you can get it in, but more likely you will bend pins if you try to force it.
What you can do first, though, is place the IC on its side, one set of pins against a flat surface, and -carefully- bend them all in a little, then do the other side. They don't need to be bent much, just a tiny bit - but once you do that, it should fit into the socket with less fuss.