look up the ideal waxing temp on the companies website, or shoot em an email, in my experience (and having talked to a swix rep), most waxes are most effectively applied between 140 and 180 degrees (depeneding on the wax composition), now this can be tough to get the right temp (unless you have a digi iron - I know swix makes em, I toko might too, but ther're expensive) so keeping your iron at the lowest temp is best bet (as said before).
Also, the holes in the iron thing. Any iron can bubble the base, but more often then not, the household irons are used at too hot a temp and seal the pores in the base shut. My understanding is that the reason that holes in an iron are bad is because they can build up wax and rust. The worst is if you get rust in your bases, you have now added corroding metal into the base material.
The way waxing works, for those that don't know, is by heating up the pores in the base, the pores open up, the wax flows in. You then scrape off what you can (which will leave the wax in the pores, this really is all the wax you need). Depending on snow conditions (how wet the snow is is actually more important than how cold the air or snow is) you might want to consider a flouro wax, high flouro for very wet, low flouro for generally wet snow, and non-flouro for those fairly dry snow (squeeks when you walk on it in your boots snow) days.
If you are going to try waxing your skis, make sure you get either a brush, or like said before a scothbrite pad. This will enable you to get the remaining wax out of the structure of the base (small grooves that allow water to flow out from under the ski). Once, you've waxed and scraped the skis, run over them with the brush or scotchbrite, use tip to tail strokes (can go tail to tip too with a brush or scotchbrite, but general rule of thumb, always go tip to tail), a couple times down the ski should get most of the wax out of the structure.
To truly know to tune, you need to understand how the ski actually slides on the snow. The wax you put on creates a controled amount of friction between the snow and ski, creating a small/thin layer of water that allows the ski to move. Depending on how hydro-phobic (water-repelling) the wax you use, and how wet the snow is will greatly effect the skis speed. The structure, small grooves, is what allows the ski to flow the small amount of water out, most of the time, a basic light structure is all that is needed.
To wax your ski properly can be a lot more involved than people realize. But once you get used to it, and understand why and how you do everything its actually pretty easy.
And remember to clean your bases before you wax. You can either use a junk wax to ''float'' the dirt and grime that may build up, or you can use a cleaner. I use Citris based stripper/cleaners, but you can also use acetone (go to the hardware store, its a crap load cheaper than going to a ski shop - people don't realize that stripper/cleaner is usually just acetone). And make sure they are good and dry before you start waxing.