If I understand your first question right...

Anything in parentheses is optional in any given syllable. So if "(C) (C) V (C) (C)" is your syllable structure, that means that every syllable must contain a vowel, and may optionally contain up to two consonants before and two consonants after the vowel. So possible syllables could include: e, be, bep, gbe, gbep, gbepn. And possible (multisyllabic) words could be anything from "io" to "bneoavklpiazr." Er. So you'd probably want to put more restrictions on it than that. Personally, I don't do complicated conlangs, but I have written random word generators to try to get a particular "feel" for my made-up names, and usually I end up defining exactly which consonants and consonant clusters are legal at the beginning, middle, and end of a word.

If "(C) (V) (C) (C) V (V) (C) (C)" is your rule for words (it's got multiple vowels, so it doesn't look like a single syllable) then "athumo" wouldn't be a legal word. It'd fill in the blanks like this:

Code:
"
(C) (V) (C) (C) V (V) (C) (C)"
 -   a   th  -  u  -   m   -
Though if your syllable rule is (C)V, athumo would be perfectly legal:
Code:
(C) V (C) V (C) V
 -  a  th u  m  o
(Assuming "th" is a single consonant, like the "th" sound in "thin".)

As for where articles and stuff goes in SOV languages...it probably varies. Maybe you could just copy what some real life SOV language does?

I hope this helps some.