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Hi guys I’m new to the manual transmission world, I just bought a standard transmission 2002 Honda Civic and I’m just getting used to driving it. My question is…. while driving, are you supposed to keep the clutch depressed as you shift to the next gear and slowly release it as you start to press down the gas pedal, or hold the clutch in then upshift and release the clutch as soon as you shift and press down the gas pedal?
this goes for up shifting and down shifting.

Can someone please give me the proper run down of how to operate a standard transmission?

 
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Start with the former. As you get better, it’ll turn into the latter. Don’t rush things or you’ll end up grinding gears.

 
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ok so In other words, the correct way to shift gears would be to hold down and slowly release the clutch and slowly press on the gas?

 
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you need to read about rev match
do you have a friend that knows how to drive a manual? ask them

it's not a one rule fits all, tons of situations and different actions needed

the only time i slowly release the clutch is in hills launch or starting moving, slip it too much and you kill the clutch early.
dump the clutch without matching revs in the engine and car jerks too much and can kill the clutch early

don't slip the clutch too much. Keep the car smooth. Speed/gear/engine revs should be synchronized
if you don't need, keep foot away from clutch pedal
don't hold the shifter if you are not shifting, shifter is not a ***** and not happy if you keep holding it

 
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I'll try to keep it simple so you don't try to process too much info.

When you start, you feel the friction point where the car begins to move forward, which is supplemented with gas when the car is moving. The same applies to upshifting. Downshifting is a bit different - I typically don't downshift unless I'm speeding up, which is accompanied by a rev-match.

This will all become second-nature eventually and you'll find things that work for you. Just a pointer - never rest your foot on the clutch pedal. As soon as you're done shifting, put your foot on the floor. This will ensure you don't burn it out prematurely.