It can be hard to know where to go with this as everyone is an individual and has personal preferences. As with all things you often have to try it to know.
Let's begin by looking at thread colour.
Try the natural colour thread on your chosen fabric (by sewing a couple of scraps together) and see what you think. If you do not like this then your easiest solution is to use a neutral grey, tan or khaki green thread colour as all of these blend pretty well with a range of tonal values and colours. Lay the individual threads across the fabric to see which disappears the most. The finer the thread the more discreet it is - one of the reasons I choose fine threads to piece with.
I personally change the thread colour often - to match the fabric. If I was sewing pink and green together I could choose either pink or green sewing thread. If, in the same project, I got to a stage where I was sewing pink and pink tog I would sew with pink thread as green thread would show up as a dirty line.
Now to talk about bobbin thread.
Whether to use the same thread top and bottom is again up to individual choice. Some machines object to different threads top and bottom and some do not. I personally use a whole range of different threads for different jobs. My 'go to' bobbin thread is Superior threads Bottomline 60 weight bobbin thread, and it will be in my bobbin for most of the sewing (quilt-making) I do . I sometimes use this in the top for piecing, but also use 100 weight silk for piecing and shiny 40 weight polyester for free-motion machine quilting. Try different threads to see what suits you/your machine best.
You can buy pre-wound bobbins but I wind my own bobbins because I always have the colour I need, and find it more immediate and easier.
Wind your bobbins evenly and 'cleanly' with no crossing threads, unevenness or ends sticking out (this will affect your stitch quality and tension). Also wind slowly, esp with polyester threads, so as not to stretch the thread and increase your bottom tension.
I suggest buying extra bobbins - that are made for exactly your make and model of machine and are not random bobbins off the shop shelf. Keep a bobbin for each of the colours you are using rather than multiple colours of thread on top of one another. This is money well spent and makes for less frustrating sewing and more success and enjoyment!