By which to take control, organising checks often to incarcerate 50% of ruffians (6,2,3,4)

'incarcerate 50 of ruffians' is the definition.
I don't know anything about this answer so I cannot judge whether this works.

'by which to take control organising checks often' is the wordplay.
I cannot quite see how this works, but
'take' could be 'r' (recipe is latin for take - r is abbreviation) and 'r' is present in the answer.
'often' could be 'oft' ('oft' can be a synonym of 'often') and 'oft' is located in the answer.
This may be the basis of clue (or it may be nonsense).

'to' acts as a link.

Can you help me to learn more?