So I want to make that rectangle mesh, which is inside of the cylinder to smoothly transition almost like the cylinder mesh is just a smooth bump over the rectangle, I'm probably going at the entire wrong way as I've only just started using blender for about a week but this one has got me stumped I've tried subsurface as I have seen that used to make the transition between a hole and a flat object smooth out but that hasn't worked, would appreciate any recommendations on how to do this.
Ok so if I understand this question correctly, you might consider using a boolean modifier. Add the boolean modifier to the rectangle, then select the cylinder mesh as the object. Use the union operation.
Check Here to see the documentation for that modifier.
It might work better to extrude the rectangle into a block, so that the current rectangle is the face closest to the cylinder, then after the union, delete the unneeded sides of the block.
Now that I understand your goal, and I tested it, I think I found what you want.
Start with a cube scaled the way you need to have the top face be your rect. Then add a low poly cylinder on top. It's key to make sure that the cylinder is more than halfway submerged in the stretched cube, as this will create a better transition later on.
After deleting or hiding the original cylinder, you might find there is an error with the polygons that make up the remaining rectangle. I found that on one side, the corner vertices were not properly connected, resulting in a u-shaped ngon. I fixed it by deleting that face, and selecting the edges I wanted, then pressing the F key to bridge them.
Select the edges of the top face of the box, and the vertical edges (Like a stick figure table). With all those edges selected, press Shift-E, and then pull the mouse away from it's starting point until the edges turn fully red. The result should look like this.
Creases won't help with the ends though. Creases are a less expensive way of controlling the smoothness, but the ends will require a more old-fashioned approach, known as control loops. While still in edit mode, create a loop with Ctrl-R. Click once while it is the center, then you can drag the loop around, so drag it close to the end to tighten up the transition and click again.