The usual way is to have a percentage which depends on the size of the job. The normal way it would be done is that (say) 5% is held back until practical completion - the point where you can move in to the house, then half of that is paid at that point, with half kept back for the defects liability period 6mths-1yr depending. The idea is that the percentage should be enough to make sure that it is worth your builder's time coming back to finish the job. In a small job, the percentage may be as high as 10% total, with 5% held back for 6mths. I'd guess that if you hadn't agreed on a defects liability period at this stage, your builder may have some issues with you now trying to impose one.
Given that it wasn't agreed before the project started, you might not get away with 10% - have a rough idea of what defects are likely, how much it would cost to get them dealt with, and use that as a bottom line.
Note: because it appears you have not used a written building contract, it is likely that you are not legally entitled to keep any money back. That only becomes an issue if things "go legal" though.