The sentence cosa credi che stessi facendo? would be interpreted like what do you think I was doing?
Adding the subject pronoun would sound very heavy and “unitalian”: *cosa credi che tu stessi facendo?, because a direct clause sharing the subject with the main proposition should have the verb at the infinitive (di + infinitive). The progressive form with the past infinitive is not used, nor it is used with the “passato remoto”.
It's quite possible that in informal speech the question could be cosa credi che stavi facendo? (there is some recent influence from English with respect to progressive forms), but the standard form is cosa credevi di fare?
Note that the usage of progressive forms differs between Italian and English; don't always try and keep English progressive forms.