You're a cyclist, and unfortunately all cyclists get spots and sores down there, with the odd saddle sore thrown in for good measure.
Firstly, if you find prefer baggies, stick with them. But wearing lycra shorts with a decent chamois will certainly help in the long term.
Use chamois creme, Assos is possibly the best – about £9 a pot, but well worth it. After you've returned from a long ride, and you've showered and what not, you could always apply some more chamois creme directly to the skin, I do this from time to time, and again it helps.
Look at your current saddle(s), do they have stitching or detailing on the area where you sit, if so then these stitches can cause a sore arse as well.
Finally, avoid standing around in your shorts after a ride, easy mistake but get out of them as soon as you can, otherwise nappy rash can result.
Was going to mention the hygiene issue, never wear dirty shorts, I'm sure you don't though.
Ciao