I've just got a new Arduino Mini Pro 3.3V that I need to solder header pins onto. I think I messed up the last one by scouring the pin terminals with a fiberglass pen which was mean to prevent the solder from forming beads and not sticking to the terminals. I think this caused some of the terminals to bridge with each other as the enamel between them was inadvertently scraped off. So, I was wondering what the proper way to do it would be? Should I use some of my electronics grade isopropyl alcohol on q-tips to clean any grease, oils or dirt off or should I use some other method to carefully physically scrub them? I thought it would be better to ask beforehand so I don't mess it up a second time! I really want to get it right this time so any advice would be appreciated, thanks.
cotton q-tip and some alchohol. rub lightly. should not need physical scrubbing.
do not apply excessive solder. the flux in the solder will help clean the pads also.
you can also apply some flux, dab some on with a flux pen, or similar.
Thanks. I don't have any flux, so I'll just have to rely on the flux inside my solder. I'll use the alcohol I have and hopefully that should work.
Good soldering is also about applying the proper amount of heat first to the connection before applying the proper amount of solder to the joint. It's really hard to teach soldering just by reading about it, but rather it's a matter of practice, practice, and more practice. Using some old discarded electronic PCB assemblies or other used electronics stuff is good practice material. It's an acquired skill and takes time to perfect. Did I mention practice helps a lot. 
Multicore solder, correct temperature, clean then tin the iron first (to tin is to add just a little multicore solder to the iron): shouldn't be any problem soldering. Apply tip of tinned iron to joint for 0.5 to 1s then press solder against iron and pin simultaneously so it rapidly melts and flows all over joint, wait about 0.5s more, remove iron and solder, job done. It can help to trap the solder between iron and the pin being soldered (which means you didn't tin the iron!)
With tarnished copper, cleaning is often needed, but tinned or gold surfaces aren't a problem in my experience.
You don't need "extra" flux, or anything special to clean the pads on your pcb.
Just re-apply the soldering iron to the pins, and the solder beads and bridges
should all disappear. You can essentially wipe away the bridges using the
soldering iron tip.
The only real trick to good solder joints is:
(a) to have the soldering iron hot enough in the first place to melt the solder in
a second or two [but not too hot],
(b) to heat up the pins "before" applying the solder, and
(c) to not apply too much solder.
Getting beads and bridges implies too much solder or the joints not being hot
enough for the solder to flow.