You can use both.. apple build their routers to work well together.. and with nobody else's.
Perhaps the TC should take the AEBS role if it is the main router.. but you can set the TC wireless to allow extend wireless.. and the AEBS to extend the wireless if you have areas of poor wireless signal.
Or you can connect them both with ethernet. Make one bridge so that there is one router still.
Whatever you do, plan to use the TC by ethernet if at all possible.. if you must use wireless make sure it is direct to to the TC, as it slows things down using double hop wireless.. ie you connect to the AEBS which then wireless connects to the TC.. each wireless hop has to happen as separate step.. packets are double handled.. it allows errors to creep in and backups get corrupted.