Reapplying MCU in new circuit once programmed?

Hello! I find my arduino very useful for early and quick prototyping, as well as programming and debugging.
But I have dabbled with making custom circuits to the point to where I can create specific circuits for my particular uses, eliminating unecessary pin usage, increasing volt and current efficiency, no longer having to rely on premade modules meant for all sorts of ratings and additional uses other than my specific needs, and resulting in a much, much smaller footprint.

So I got a standalone ATMega328p preloaded with a bootloader for arduino use, a timing crystal and I already have plenty of capacitors.

So I am wondering, is there any issue I might not be aware with the Arduino Uno setup, or can I use the arduino to program, test and debug, then simply transfer the ATMega to a custom circuit using the same pins?

Should work fine. That said, I would consider breaking out a 6-pin FTDI-style connector for serial programming (including the DTR reset circuit - 10k resistor from reset to vcc, 0.1uf cap, one side connected to reset, other side to DTR of the FTDI header) or ISP header, unless you're only going to program it a few times. Debug cycle that involves inserting and removing the chip from a socket is tedious, and you'll eventually slip and mangle the pins on the IC. On the other hand, it can be a bit of a pain to wire it up by hand.

Graylord:
So I got a standalone ATMega328p preloaded with a bootloader for arduino use, a timing crystal and I already have plenty of capacitors.

Remember (these are things that many guides omit):
0.1uF cap between Vcc and Gnd right next to chip
0.1uF cap between AVcc and Gnd right next to chip
AVcc connected to Vcc
ARef NOT connected to Vcc
Appropriate caps for the crystal (18 or 20pf is the norm here).

All the caps listed above should be ceramic.

BTW, if you're looking for some spiffy prototyping board to make your '328p projects on, I happen to sell some.

Alright, Thanks! I think I'll actually consider using your 40-pin board (so that I have space to add some more functionality on the same board). Is it spaced so that you can fit a dip mount chip in the middle, but leave the 2 central buses open? I'd like to have 2 positive buses at different voltages (regulated and unregulated) with a common ground on the same board, the amount of buses on your board seems to support this nicely.

I'll also get back to you once I start hooking things up, so that I can get confirmation if I am missing something or if it looks fine.

DrAzzy:
0.1uF cap between Vcc and Gnd right next to chip
0.1uF cap between AVcc and Gnd right next to chip

Wouldn’t one of these suffice? In practice the closest position on my board for each of these are right next to eachother. They connect to the same 5v source and ground rail.

Graylord:
Wouldn't one of these suffice? In practice the closest position on my board for each of these are right next to eachother. They connect to the same 5v source and ground rail.

Some people do that if AVcc is hardwired to Vcc (as it normally is; Atmel recommends a small inductor between Vcc and AVcc (in which case you definitely do need the two caps) though 99% of designs don't do that. I do not approve of this - caps are SO cheap, and decoupling cap related problems are SO hard to debug.

Normally one should be on each side of the '328p, right next to it; the caps would not be next to eachother. They should not be off to the side on the power rails; they will not do their job if they are not right next to the chip! I have had failures due to the length of traces to a cap. Had to do a respin and throw out a batch of boards. Really drove home the importance of decoupling (wasted ages debugging it too).

I see, I'll see if I can get the capacitors close to the pins somehow.

Graylord:
I see, I'll see if I can get the capacitors close to the pins somehow.

On one side of (DIP) ATMega there is Vcc pin next to GND pin. It is easy to solder a small SMD ceramic cap between them from the bottom of the board.

If it's the through-hole version, you can solder a through-hole ceramic cap to the ends of the pins on the underside of the board. On the SMD one, it's harder. I have soldered components to the top of the pins of an SMD '328p. It's not fun, but it's doable (when I discovered the problem I mentioned above, I tested it by soldering a cap across the top of the chip on the one I'd assembled). Secure them (presumably to the top of the chip) with hot-melt glue after you get them soldered on - solder joints like that break very easily if the component/wire isn't secured.