Bit of honesty in this reply as I rather think you've not done any research into SS2 yet.
SS1 and SS2 are entirely different beasts.
You cannot install SS2 into a game that had SS1 active. this is written clearly in the sticky posts on the mod page. This is literally the first thing you need to comprehend. You will need a brand new game. No arguments, that's how it works.
Note, if SS1 is slow on your current system, you'll get the same and probably worse performance out of SS2. It is a very, very script heavy mod that will give you a whole load of nightmares, including when you first start a new game and find that the game doesn't even load the files correctly.
There are scores of posts in these forums detailing that and a myriad of other issues. Read them and understand what you need to do to get SS2 installed and a game started.
My advice - do your research before you dive into SS2 - and do not expect a wonderful gaming experience. It isn't that, or anything near that. At all.
It is a frustrating, bug-riddled mess that is incompatible with a few commonly used mods, thus making the experience all the more painful. The bugs are being worked on, and each iteration makes the SS2 mod better, but it's extremely painful out of the box and continues to be painful due to lack of clear mechanics and clumsy interactions that are caused by game engine limitations.
One other thing, in your post above you indicate settlers building over items you've placed. Simple answer to that is don't place stuff in or on or nearby plots. each plot comes with a border - simply build from the border out. Don't build over the border into the plot itself.