Hi, I would remove any perennial weeds and large stones before rotavating, as if you do it first you will just cut up the roots of perennial weeds, and also possibly damage the blades of your rotavator,.
I think you're probably thinking of a herringbone drainage system with the pipes, but that is quite a big job, which includes a lot of digging of trenches, which are gradually deeper towards the central ,larger pipe, and can be done with either clay drainage pipes, [which are expensive] or plastic piping with slits cut into them, it's no use putting vertical pipes under the top surface, they would just fill with water, as it has nowhere to go, other than that, your plan is ok. Derek.

Hi Derek, thanks for the advice mate, I have built a new soakaway below where those blank dustbins are in the picture as we also having an extension done and needed a new soak-away, wondering if I could get some perforated pipes dug around the garden all running down toward the soak-away?

Hi, If you already have the soakaway, you have nothing to lose by putting slitted pipes in, just make sure that you have enough of an angle to keep the excess water flowing and not just sitting around, once you have them in place cover them with pea gravel to stop the slits getting blocked, Derek.