EOD manifest & 1st class letters

I am sure have read others have this issue but cannot find the posts. I have been sending all post rm24 / 48 but now have a few products that can go letter. I have our RM account linked to amazon and so the cost of post is invoiced directly through RM.

Today I have processed some of the letters but have noticed the cost of the standard £1.10 not the rate I have with RM. Also noticed the letters have not appeared on the end of day manifest.

We dispatched about 7 bags full and so by the time I realised didn’t have the time to fish them all out before collection so they have headed to royal mail. Meaning i am expecting a fine for extra post.

Have I done something wrong. should these be separate? How am i being invoiced for them?