The library supports writing to plain Mifare cards as well. Have a look at the mifareclassic_memdump for example and you can substitute the read commands with the write function:
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uint8_t Adafruit_NFCShield_I2C::mifareclassic_WriteDataBlock (uint8_t blockNumber, uint8_t * data)
You first need to authenticate the block.
As for NDEF, use this with care since you need to change the authentication keys for NDEF support. You CAN still write to the blocks, but they keys will be different, and you should probably consider the format one way and keep separate NDEF and pure Mifare Classic cards for convenience sake.
Have a look here as well as the NDEF page just after this one: http://learn.adafruit.com/adafruit-pn53 ... nfc/mifare