Couple quick questions, I'm new to the mod, been bouncing back and forth between Prince and Emperor (Prince for warring Civs, I just can't seem to get Authority tree down well.)
1.) Is settling on fresh water/hills as important as it was in standard Civ? I notice the Well building seems to indicate that settling off water might be okay in many instances, just confirming.
Depends on the civ you're playing, but generally no, not really. Main advantage of settling on the river is the Baths building.
2.) Is it still ideal to just chop trees? And how important is it to save jungles if you don't need to chop them?
Depends on the civ you're playing and the strategy you're employing. I usually cut down most the trees to get more farms, but if the location is slightly isolated so I can't get a good farm there I usually leave the forest.
3.) Do you typically default to making your first few trade routes just internal food routes? Or is it viable or more ideal to do other things?
I usually send international trade-route, and my first few usually try to hit city-states with trade-route quests. If I don't have any of those I usually go for the highest science route I can establish (assuming the gold is fine).
4.) Is it still correct to force new workers to do production via the city manager and then lock them to a different tile?
This 'trick' doesn't work in CBO, the order the yields are calculated have been intentionally changed so people can't exploit that anymore. So to answer your question, no.
5.) I notice the City manager loves to work specialists, often to the complete detriment of growth. I can't seem to break my old habit of just working scientists and not sure how important other specialists really are in this version. Any rule of thumbs here?
If you're playing tradition, be sure to manually lock specialists, the automation can really mess you up with so many specialists to choose from. Personal tradition strategy involves manually locking engineers and culture-based specialists and setting the city to food-focus, getting scientists in there once the city is big enough to sustain them and still grow.
For non-tradition games, the important part is still to make sure your cities grow big enough to actually work the specialists. In CBO all specialists are decent to work by themselves, and all great people are fantastic (and unlike vanilla getting a great merchant doesn't slow down your great scientist production), this means that you generally want to work as many specialists as you can. Which specialists to prioritize kinda depends on the situation, if you're going really wide you're kinda forced to work all scientists in all cities to keep up, for example.
Sorry for the generic questions, some may have already been addressed. But, I'm in the "breaking old habits" mode here, and trying to adjust. Thank you!
No problems, I'm sorry I can't really give you more specific answers, CBO to me is a lot of instinct.