[yuriyuri]

The . is there to tell you where the kanji reading ends
少ない
すく・ない
means that 少 in this case is read as すく

In my opinion there is no "proper process", I personally just learn readings as I come across words.
After a while you start being able to guess what readings to use with some decent accuracy.

Depending on the word the reading might change, and this is where you would look at the kana that makes up the rest of the word.

For example:
少ない　（すく・ない）
少し　（すこ・し）

I tried to memorise on and kun readings for each kanji but it was driving me insane.
I personally find that simply reading every day does the trick.

I'm not sure if I mis-understood your post but I hope this helped you a bit.