In the stem of the word, it's basically just memorising.
It's like "ee" versus "ea" in English -- they used to be pronounced differently, which is why they are spelled differently, and then the pronunciation merged but the spelling stayed separate. And so you have to memorise that "meet" (= encounter) and "meat" (= flesh) are spelled the way they are, and similarly in Greek with nouns such as χώρος (place) versus χορός (dance).
In a grammatical ending, you can use grammar to help you; for example, the verb ending for εγώ is spelled with -ω, while the masculine (second declension) noun ending is spelled with -ος, and so on.
So while you can't guess the vowel in the θρόν- part (you simply have to memorise it), you can be pretty sure that the -ος has an omicron.
You may encounter similar difficulties with ε, αι and with η, ι, υ, ει, οι -- but there, sometimes it can help to know how English spells the appropriate loanword. (For example, knowing the κοιμητήριον is spelled "cemetery" in Greek lets you know that the first three syllables can't contain ι or υ, because otherwise English would have spelled them with "i" or "y".)