setting up a brand new Arduino

I think there are a lot of us out there crying for help. I just purchased the Arduino Uno R3. Got it used. No documentation at all. Arduino site is extensive; I could read it for weeks and not find the answer to my questions. As a former engineer with GE Ordnance Systems, I am not totally ignorant when it comes to electronics, electro-mechanics,etc. So Vasquo recommended being specific so, here goes.

Question #1: Other than the pins used for interfacing with shields, I count 12 pins that are a mystery. 6 marked ICSP near the ON led and 6 unmarked pins near the pin 13 blinker led. What are they for specifically? In setting up the Arduino for use, do I need to do anything with these pins, jumperswise?

Question #2: I have read in a least three places where when updating the software in the Arduino, one must thoroughly remove any previous version of the software (ie grbl).Nowhere, however, have I seen any instruction on how to do that.

There will be more questions as I

Short: only connect the USB cable to the computer and you should be good to go.

Longer:

You can find the schematic for the R3 here. You can follow the lines for the ICSP and will find that they are connected to the 328 micro but also to the (normal) IO headers. ICSP stands for InCircuit Serial Programmer and you can use it to directly program the 328 micro without need for USB); under normal circumstances there is no need to use it. Instead of having to put loose wires into the IO headers, you have a nice centralised place to connect everything needed for InCircuit programming using a e.g. a flatcable and correct female connectors. You can use it to connect something that requires those pins (I think it's the SPI interface but not sure).

Under normal circumstances you will load code using the USB connection and you don't need the ICSP. The other pack of 6 that you're referring to is probably ICSP1 and as far as I understand it it will be used to reprogram the 16U2 micro (that usually takes care of the USB connectivity). Normally not used.

For question 2, please provide a link; I think the wrote BS. I'm relatively new to Arduino but I have never had to thoroughly remove the previous code.

There are 2 ICSP connectors.1. for ATmega16U2 which acts as USB/serial tranceiver and to be able load the firmware. 2. is for the main MCU - ATmega328P. They are duplicated with pins on headers. It is used to load the bootloader.

Q2: Normally during new sketch upload, the flash is erased first. You need not to do additional action. You can switch on verbose mode in the preferences to examine the commands called from IDE during uploading.