Normally an Access course consists of some level two work, normally this is some basic maths and english, some colleges also offer ICT as well. All your work in these basic subjects will be marked and graded at level 2. It is not possible to get higher than level two in these subjects.
In the more complex subjects you will be marked at level 3. Level 3 work is then split in to 3 categories, Pass being the lowest, Merit being the middle, Distinction being the best. Think of it as being awarded an A, B or C.
So in terms of
"Normally we require 15 credits at level 2 and 45 at level 3 of which at least 39 level 3 credits should be graded at merit or above"
Presuming this is what a university has told you, this means that they would like you to pass the access course with 15 credits at level 2, these come from the easier maths, english and ict units tha you do. 45 credits at level 3, these come from the more complex subjects, they would like you to have achieved merit in 39 of those 45 credits.
Each college is different. For example, 45 credits for me is made up of 15 assignments worth 3 credits each. Best checking with your individual subject tutors to see how many credits are available in each subject and how they are broken down