Using PwnageTool to upgrade will preserve your jailbreak and ultrasn0w unlock. If you are using the blacksn0w unlock at baseband 05.11.07 you will need to stay at 3.1.2.
As always, we will update our tutorials shortly :-)
iPhone 3GS users (regardless of unlock) should stay away from this and all 3.1.3 jailbreak tools unless you know you have your SHSH hashes backed up via Cydia. Thats because if you make a mistake you may find yourself stuck at official 3.1.3 with no way to jailbreak or come back down to 3.1.2 to jailbreak.
If you really truly feel that you need to update, this version creates a custom 3.1.3 IPSW for you to restore to on your iPhone 2G, iPhone 3G, iPhone 3GS with early bootrom, iPod touch 1G, and iPod touch 2G with early bootrom. If you dont know if you have an early bootrom or not, please avoid updating until you learn more.
You dont need to be pre-jailbroken on anything but the iPod touch 2G early bootrom. And really for that device, its faster and easier to use redsn0w 0.9.4 as mentioned in our last post. For that matter, if you have an ipt1g, iphone2g, or iphone3g(and dont need an unlock), you should use redsn0w too (but version 0.9.3). Its faster and you wont have to go through a full restore process (just do an update then run redsn0w, pointing it at 3.1.2 FW instead of 3.1.3).
If you have an iPhone 3GS, PwnageTool works if youre currently at version 3.1.2 or below (down to 3.0). You dont need to be already jailbroken PwnageTool will ask you if youre jailbroken after youve created the IPSW. Dont use PwnageTool on the iPhone 3GS if youre at 3.1.3, it just wont work. Downgrade to 3.1.2 using the methods described here. If you cant downgrade because you dont have your 3GS 3.1.2 hashes on file with Cydia, youll need to sit out the 3.1.3 jailbreak.
You can download PwnageTool 3.1.5 from here