All future payments related to the lease must be done by bank transfer directly to the bank account of your landlord.
In advance you can find out how to make a foreign bank transfer to Czech Republic by asking in your bank. The final amount must be credited in CZK and it must be the exact amount of your rent. All bank fees must be offended by you.
In case you do not want to make a bank transfer for any reason, you can use the second option of paying the rent. You can withdraw the amount from ATM and put it in cash to the landlord's bank account. You need to visit any branch of the bank written in your contract and ask there to credit the money to the bank account also written in the contract. The bank fee will be much lower. You always need to write your name to the note, so the landlord knows who paid.