That's easy: just read through your own handwriting, until you stumble onto 12 words that form an incoherent sentence. It might take you a few hours, but you'll find it.
well yeah but if someone else found the diary they would do the same exact thing.
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That's true. And that's why I wouldn't suggest adding your own encoding, just keep the 12 words together. I'll give you a hint: search for "Blanket" on this page 
a reasonably sophistocated attacker would simply get the diary into a text file then search for strings of keywords in the bip 39 wordlist. "blanket air setup scrap feature actress prison bitter cash torch vacant valley" would stick out like a sore thumb. so keeping the 12 words together would be like handing over your seed phrase to an attacker on a silver platter.
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That's because I couldn't find a meaningful diary to download as an example 
In real life, if you have a diary already, you can just add the seed words today in the middle of your story. The coming months it will be hidden "deeper".
not really. an attacker will just be even more motivated to crack your diary. the bigger it is the more exciting for them. especially if they think there is any type of anomoly with your diary like you are trying to hide some type of information or the diary entries don't make sense. and yes they really will read through every page of it to see if that's the case. In real life, if you have a diary already, you can just add the seed words today in the middle of your story. The coming months it will be hidden "deeper".