After playing, swab out your flute body and head joint, and blot the pads dry before putting it back into the case. It is best if you can do this after every time you play. Once a week, clean the head joint embouchure hole [chimney], and use Yamaha Powder Paper on the pads if you have issues with "smacking pads".
Swab out your flute body and head joint using an absorbent cloth on a cleaning rod or a flute flag. Cleaning cloth material vary in absorbency and hardness in fibre. Microfiber cloths are very absorbent [up to 60 times as absorbent as cotton] and soft. A small amount, like the "flag" on the flute flag is sufficient. Cotton, silk, and linen are also good. They are less absorbent so require a larger cloth. Silk and linen are harder fibres, and as such are less absorbent so a very large piece is required but will polish the inside better than any material I recommend. You can experiment and see what works best for you. On plated instruments, one of the softer materials may be a better choice.
Use lens towel from Lenscrafters or Pearl Vision Centre torn into pad width strips or Yamaha Pad Cleaning Paper to blot the pads dry. Insert the paper between the pad and tone hole and close the key so the paper is pinched between the pad face and the tone hole face, then release the key.