Just wondering if I should agitate the carboy during fermentation/towards the end when it starts to slow?
You can if you want. I find it to be helpful sometimes in knocking the krausen back down so the yeast will settle out sooner.
Also, I sometimes swirl the fermenter gently to blend some yeast back into suspension on purpose to ensure full attenuation for yeasts that flocculate too quickly.
Use your best judgment. If you think you should, I say go ahead and do it. Just be gentle so that you aren't adding a lot of oxygen back in, as that could lead to faster staling.