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Thanks all for your replies,by miracle i finally got things sending right template but still makes no sense, still trying to work out where the info is being pulled out from. So as test I tried to modify the order_conf.txt, just adding some dummy text that should show up even in the admin preview. So here are all the paths I have tried 

/mails/fr/order_conf.txt (i know this should not exist but i tried just in case)
/mails/themes/classic/mails/fr/order_conf.txt

/mails/themes/MyCustomTheme/mails/fr/order_conf.txt
/themes/MyCustomTheme/mails/fr/order_conf.txt

Cleared cache and refreshed after each change, why the hell I am not seeing the changes yet ... driving me mad 🙂

Is there some cache to be cleared in the admin ? Because i see that when I preview the url is adminxxxx/improve/design/mail_theme/preview/classic

Thanks all for your replies,by miracle i finally got things sending right template but still makes no sense, still trying to work out where the info is being pulled out from. So as test I tried to modify the order_conf.txt, just adding some dummy text that should show up even in the admin preview. So here are all the paths I have tried 

/mails/fr/order_conf.txt (i know this should not exist but i tried just in case)
/mails/themes/classic/mails/fr/order_conf.txt

/mails/themes/MyCustomTheme/mails/fr/order_conf.txt
/themes/MyCustomTheme/mails/fr/order_conf.txt

Cleared cache and refreshed after each change, why the hell I am not seeing the changes yet ... driving me mad 🙂

Thanks all for your replies, I think I am getting there, i think that the most confusing is the BO theme email section, i thought that as long as you had a /mails folder in the custom theme this would be taken in priority. In the BO you have to first select a default email theme and the only options you have are the core ones, then you have to "generate emails" from a theme, pick a language and select a theme to overwrite, this is what confuses me, I want in the first place to use the email theme from my custom theme which is not on the list, anyways, maybe it's my understanding, I finally got the right templates to be sent, but have to do some cleaning because I am sill not sure whre they are coming from because it started working when I changed things withing the themes/customethemes/mails, but in the BO all options are set to classic , but a bit of reverse engineering should answer my doubts now 🙂 Thanks a lot all for your input 

Thanks all for your replies, but still a bit confused as to what i am supposed to do now that I have put my .txt and .html files in the classic/mails folder, what is it that goes in templates/layouts/components ? Apart from footer and header, what is it that needs to be tweaked there so that the .txt and .html templates are rendered properly ?  Where is this pointing to when I go ni the BO and preview the template :  "improve/design/mail_theme/raw/fr-FR/classic/bankwire.txt"