My question involves criminal law for the state of: California

I was caught stealing 150 dollars worth from sears and i got arrested and had to get bailed out. they charged me with a 459 burglary and felony. i am a 1st offender and i dnt understand y they would say its a felony. shouldnt it b petty theft and a misd? i got a letter from there lawyer talking about the penal code 490.5. they want me 2 pay 400 and it says that the payment demanded made uopn me does not prevent criminal prosecution under a related criminal statute provision. what does that mean? it also says that i should pay the amount or they may hire a civil counsel and take more legal steps. does that mean that im being charged with both penal codes 459 and 490.5? am i going to go to jail again?