I use the full logic so assume its pretty close, but you should go search on the internet and learn about EQ, compression, different effects, and maybe think about downloading more plugins than just the stock ones in logic, although they are fairly good.
As for clipping, just turn it all down. Compression will help with that to some extent but really everythings probably just too loud. Automation of volume and effects can also help control peaks and shit... If you are actually looking to master you bring some volume back in that process, so its okay its not as loud as you think it should be. Key is a good unclipping mix.