This is how it works...
Normally you would check in using UK passport, and when/if asked for Visa just show Thai passport. Clear UK immigration with UK passport, then put it away.
Then use only Thai passport show at Thai Immigration.
But as you mentioned, you uploaded the Thai passport info into the Airline system, so this what they will expect to see (but they could ask for UK passport for ID check). But clear UK immigration with your UK passport, and then of course Thai passport at SUV.
PS::::: I am not from UK but this is the exact method I use when travelling with 2 passports to my country.
Hope this helps.