Should I transplant germinated seeds or place them straight into pots? Also xtra tips

I have just germinated autoflowering seeds for an indoor grow. I have 3 gallon air pots and organic soil/nutrients. Should I plant them in the pots or solo cups to start? What are the pros and cons of doing this? I've read many mixed opinions on either method. Also, I have a 400w MH light, 1000w HPS and T5 lights. (not including my CFL's 2700K) Which light source would be best for the young seedlings to grow? How much light/hours daily?

-Also if anyone can help me with my current plants that have already been growing for 65 days now, I transferred them from outside to my indoor setup. I have two autos with buds on them, and one photoperiod that hasn't formed any buds yet. I've been switching every other day from my MH to my HPS because I feel one needs veg one needs HPS?I keep my T5 lights on all the time near the underfoilage (except at night). How should I introduce these new seedlings into the grow room with the lighting phases I have going on? I'm already trying to time the autos alongside the photoperiod plant...I want the photoperiod plant to start producing buds asap so I can focus on these 6 new autos.

I appreciate any help..first time grow this summer outside now first time grow inside.

the rule of thumb for autoflowers is to plant in the final pot, so put them in your 3 gallon pots.

use the T5's for the babies, MH for veg...then HPS for flower

with autoflowers....most go with 18/6 or 20/4 from start to finish

ISK is correct. I usually transplant them directly into whatever I'll be flowering them in so as not to risk any transplant shock. The only upside to upgrading from solo, to 1 gal etc. is having a chance to add amended soil. This is only really important when using organic soil. So, toss em in some 3gal pots and you'll be set. 5gal pots are even better. Give those roots all the space they need!