Do what you need to do first in SFDC. Any new fields your thinking about, do it now. (you can always add more custom fields in SFDC and they will get come over to Marketo automatically on the next Sync).
Creating a new field in Marketo does not create a field in SFDC. Its the other way around. (unless of course you dont need to send the collected data to SFDC, then your fine).
Now that your about to sync the two platforms together, you get the chance to re-map fields that your not happy with from the 'Out of the box' mapping. When your done it can't be undone by an admin in Marketo, will need to get Marketo support to help out. (unless this has changed recently.
Here is the Marketo Lead Management instal by SFDC Edition:
http://community.marketo.com/MarketoTutorial?id=kA250000000KywpCAC