If there are header pins, what is the purpose of the iscp? For example, when you are connecting the miso pin, would you be able to connect to either the pin header or iscp header?
Or is there a specific header for the iscp?
The ICSP header just makes it easier, quicker and less error prone to connect a programming device to a target board.
By having a standard pinout for an ICSP header, a single programmer (and programming cable) can support many different variations of a particular microcontroller, as is the case for the AVR devices.
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Alright thank you, that makes sense!
To confirm, my goal is to recreate an arduino board and I'm finding a 2x3 header pin, can I use any 2x3 pin header, and connect traces to MISO, VCC, etc., instead of using an avr isp?
Yes.
Just make sure you follow the proper pinout. It's designed to work in one way, and not break things (no risk of reverse polarity where it matters) when you connect it the wrong way around.
I often don't populate the header, using a 2x3 pogopin connector instead to make the contact when programming. Particularly useful for programming the second and following boards of the same design.
Otherwise indeed a 2x3 male connector, like you also find on the Nano. Then you can connect it directly to a USBASP device, and program straight from the IDE. Those programmers are dirt cheap.
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For boards that follow the Uno form factor, the ICSP header is also the only place that is guaranteed to carry the SPI signals. Check the pinout of the Uno versus e.g. Leonardo and Mega ; the Uno has the SPI signals on pins 11, 12 and 13, the Leonardo and Mega don't.
I am following the micro form factor! I checked which pins are the spi pins
can you explain a bit more why the icsp header is the "only place that is guaranteed to carry the SPI signals"? I'm hearing different things regarding if other headers do/don't work 
I am currently using DZ127S-22-06-55 | DEALON | Pin Headers | JLCPCB, would this be acceptable? I'm trying to get components that are compatible with jlcpcb
That pin header is a surface mount type rather than a through hole type. Personally I would use a through hole part for the additional mechanical strength.
If I read the part correctly, then it has a 1.27mm pin pitch. This is different to the Arduino UNO ICSP header which has a 2.54mm (0.1in) pin pitch.
A quick look on JLCPCB and I think you should search for a pin header with a 2.54mm pitch with 2x3pin layout.
I see, I don't own a programming cable so I was just planning to connect an arduino and my prototype with jumper wires. I also only intend to use these pins once, so I chose smt. Would using the aforementioned component still be a fine option? (I'm still a little confused because of the other point that was brought up--if I need to explicitly use an icsp header or if any header works).
If not, I'll look for another component with those specs!
Thank you everyone so much for the help so far!
There is nothing special about an ICSP header. It's just a 2x3 pin header on a 2.54mm pitch wired up with the appropriate signals and power.
You could use a 1x6 header if you wished. It would still be an ICSP header, just not compatible with the programmers that have a 2x3 connector. You could make an adapter cable for your particular header.
If you are using jumper wires, then stick to 2.54mm pitch as the jumper wires will fit the header.
In that case it does not apply.
The three boards I mentioned all have the ICSP header that carries the SPI signals. The Uno hs those signals on pins 11/12/13 as well, the Mega and Leonardo don't have the SPI signals on 11/12/13.
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The same applies for the I2C bus.
On the Uno, the I2C signals are available on A4/A5, on the other two boards they are not.
When Arduino started expanding their range of boards, they needed a standard place for the I2C bus (or sacrifice (analogue) pin functionality on A4/A5); and hence the SDA/SCL pins on the header that also carries D8-D13 were born.
Uno
Duemilanove (one of the Uno predecessors)
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