Learning chemistry with software?
Do your chair parade.  See what the Kahn Academy has to offer.  Have more than one texbook.  If organic is not the best thing in the world pursued clothed, consider other options.  Employment at the bench will be under management that has other goals.  Grant funding considers discovery to be unacceptable risk.  Remember what they called the first designed degenerate Cope rearrangement - BULLVALENE.  It worked.  So did its two-step synthesis using no reagents.

LCAO for hybridization, geometry, resonance, and 1,3-shifts.  Nomenclature and chirality.  Woodward-Hoffmann comes later.  Carbocations, carbanions, radicals.  Carbonyl condensations.  Hard and soft acids and bases, Lewis and Brønsted acids and bases.  Reductants and oxidants; reagents in general.  Name reactions (that you already know as pedagogy).  Practice looking into stereograms.

NMR, IR, UV-Vis (not so much now), mass spec with database and software.  You should have some glassblowing under your belt - Schlenkware;  T-, butt, and ring seals; making an ampoule.  Own your own didymium glasses and Kennametal cutter.  Burn a pencil for its "lead."

Synthesis.  Work backwards via the synthon approach.  We used to read the new Aldrich catalog, and Fieser and Fieser, but both have has gotten out of hand.  Spend a weekend/month skimming the main journals - JACS, Angew. Chemie, JOC, Tetrahedron - and what interests you.  Never fill a reaction flask more than half full, because the universe hates you.  COTTON lab coats, because they don't melt onto your flesh.  Don't do anything stupid twice.  When in doubt - palladium.

Buy HyperChem Lite, oh yes indeed.  Remember to add hydrogens, assign atom types, then minimize well below the recommended cutoff for 10 times the recommended iterations, at least.  Note how the software is boggled when minimizing high symmetry cage ketones 

If it isn't fun, you might be a theorist.  There is no shame in that - but you don't get to make crystals.