If all you're going to do is replace the timing chain, with the timing cover off, rotate the engine so the dots line up. THEN remove the timing chain. Slide the lower gear on with the Zero dot up. If the bolts don't line up it is because the chain was really loose causing the cam to retard a few degrees. If you are running a real big turbo and it feels lazy, you can advance the cam 4* and get a little bottom end back. If it is a fairly small turbo (PT54 or smaller) keep the timing straight up.
If the bolt holes are off alot, there is a machining problem and the best bet is to degree the cam in. Pretty hard to degree the stock cam because we don't have a cam card to go by.
I have a few sets of NEW GM timing chains and gear sets with dampnners if you want to just slide it all back together with the exact factory parts. The stock timing chans are a nice part contrary to what even I use to think.
Just this last week I had a Rollmaster timing chain failure. Two of the rollers had broken off and others were cracked. The link pins were all good and it was VERY difficult to even see the missing rollers. I was rebuilding a low mile engine and reused the timing chain set. It was still tight and looked good. IT only had about 10,000 miles or less on it. After the engine was completely assembled and only needed the oil pan installed, I wiped the pan out and found the pieces. Took a bit to figure out what happened. They were bigger in diameter than a new chans rollers, so I thought it was a roller tip from the rockers. But they had expanded after they split, so they were larger than the original. I pulled the fuel pump block off plate and rolled the engine over and saw the missing rollers. So off it came and a new one installed. So always check the timing chains CAREFULLY with a bright light EVERY time you disassemble the timing cover. I will always just replace it at each tear down, even if it only a few thousand miles on it. $125 is cheap insurance. There just isn't a good high quality chain available for the Buick V6. Good luck with your build.