Copying a passage and explaining its meaning are different tasks. Keeping them distinct makes a research note easier to review. A later reader should be able to see where the source ends and where your own reasoning begins.
Give the copied passage a clear label and record its location. Mark anything you cannot read instead of silently supplying a plausible word. If you make a modernised reading for convenience, keep it separate from the closer transcription.

In another paragraph, describe what you think the passage suggests. Explain the steps that connect the wording to your interpretation, including any context still missing. An uncertain reading should remain visible even when one explanation seems especially attractive.
Return to the note when new material appears. You may revise the interpretation while leaving the recorded wording unchanged. This arrangement preserves the path of the enquiry and makes it easier to recognise how your understanding developed over time.