You can use BrokerTransmit and AutoTrading in the same account however we should point out a couple of limitions:
You cannot check off the same instrument(s) in BrokerTransmit that you are already AutoTrading.
Example: You cannot check off stocks for BrokerTransmit while AutoTrading a stock strategy.
BrokerTransmit allows you(via Broker Transmit setup page) to place manual trades for the checked off instrument(s) in your account that you are AutoTrading and it will not disable sync. If you place a manual trade of an instrument that is not checked off for BrokerTransmit, AutoSync will be disabled.
Example: You checked off stocks for BrokerTransmit and place a manual trade for an option trade in your broker account. AutoSync for your AutoTrading will be disabled.