Q. One who is considering becoming a baal teshuva from scratch, he doesn’t yet keep Shabbos, kashrus, taharas hamishpocho etc. etc. should he now put on tefilin, tzitzis, daven and do other mitzvos, since the mitzvos may go to feed the klippois and the sitra acher and better wait until later?

A. In principle a sinner should indeed first repent and then proceed to do mitzvos and good deeds, as the pasuk (Tehilim 34: 15 ) teaches “sur mera vease tov – depart from evil and do good.” He may also incur into: But to the wicked man Hashem said, “For what reason do you recount My statutes, and bring up My covenant on Your mouth? (Tehilim 50: 16).
Rambam (H. Teshuva 7: 7) similarly writes; How sublime is the elated Teshuva; yesterday (the sinner) was isolated from Hashem, the G-d of Israel… he would cry out, but was not answered… he would perform mitzvos, and they would be thrown back into his face, as it is written; (Yeshayahu 1: 12) When you come to appear before Me, who requested this of you, to trample My courts?
Many Cabbala and Musar sefarim do stress how nefarious and damaging could be the mitzvos that are created in a state of impurity. (see Beir Heitev O.H. 571, Shaar Hayechudim from Rav Chaim Vital, introduction to Drerech Pikudecha, et. al.)
However, they also assert that when teshuva is eventually accomplished, they all can return to the source and roots of kedusha.
Beis Halevy (Itroduction to Perush on Torah) quotes a parable of the Yalkut (Shimoni, Hoshea 529), that compares a Rosho performing mitzvos, to the one who has saved rusty, damaged coins, that merchants wont accept. Eventually when he has many, and he encounters a money-changer, he may change them by paying an extra bonus of the same coins to obtain a lesser amount of viable and worthy circulating coins. However, the one who didn’t save any coins because he thought they were all faulty and undesirable, has nothing to exchange, and sadly remains destitute.
Horav Shlomo Miller Shlit’a also pointed out that he is obligated at all times to comply with all mitzvos, besides “mitzva goreres mitzva – one mitzva causes and brings to others.” Eventually his Torah learning, tefilos and mitzvos will be the tools needed to guide him and encourage him back into complete teshuva.

Rabbi A. Bartfeld as revised by Horav Shlomo Miller Shlit’a