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