1. We put “wa” after “watashi” and “ga” after “asagohan”. Particles in Japanese are post-positions – they modify the word that comes before them. Particles in Japanese indicate the function the word plays in the sentence – so long as you keep the same particle with the same word, you can rearrange the sentence as much as you like, and not change the meaning of the sentence (though note if you jumble it up too much, people will lose track of what you’re trying to say).

2. You can have two “wa” particles when “wa” is functioning as a contrastive marker. The grammar dictionary explains that “when more than one wa appears in a sentence, the first wa is usually understood to be the topic marker, the second wa is more contrastive than the first one, the third one is more contrastive than the second, and so on”. It then goes to give the example “watashi wa kyou wa tenisu wa shinai” (I won’t play tennis today), though I have to admit, I’m not quite sure whether it’s saying that I’d prefer to play something else today more than tennis some other day, or the vice versa.

Note that you probably won’t encounter a sentence so wa-heavy in real life. Something slighly more realistic would be “otouto wa asagohan ga kirai jyaarimasen ga, watashi wa kirai desu” (My brother doesn’t dislike breakfast, but I do). By the way, the “ga” before the comma is a different particle to the subject marker “ga”, which you’ll be learning about later. Means “but”.

Two “ga” subject marker particles in a sentence is a little more frequent, as “ga” always marks the subject in subordinate clauses (unless that subject is being contrasted).

3. As I’m pretty sure I’ve mentioned to you before, the A wa B ga C structure is one of the standard basic grammar structures in Japanese, which you’re going to see fairly often. You COULD say B ga A wa C (cf note above about particles) but it’s not very natural, so you’re going to get funny looks. Note that A ga B wa C changes the meaning.

The grammar dictionary says “C usually expresses something about B, and ‘B ga C’ expresses something about A”. It goes on to explain there’s basically three categories into which sentences of this structure fall:

a) A is human, and B ga C expresses something about A’s physical and/or mental state – for example, “watashi wa eigo ga wakarimasu” (I understand English) or “otouto wa asagohan ga kiraijanai desu”.
b) B is part of A, and C says something about B, which in turn says something about A – for example, “Maikeru-san wa se ga takai desu” (Michael is tall) or “watashi wa onaka ga suita” (I’m hungry – literally, my stomach is empty).
c) B is a member of A, and C expresses something about B – for example, “jisho wa webusutaa ga iidesu” (On the topic of dictionaries, Webster’s is good

It then goes on to give a list of verbs and adjectives that almost always take the A wa B ga C structure, like “wakaru” or “hoshii” or “suki” or “hazukashii”. And so forth.

Hope this is actually helping, and not just confusing matters further.