Hi,
Whilst getting into macro mode will give shallow depth of field (DOF) because of the close distance the general rules of photography/light still apply... So for example to maximise the depth of field you would want the slowest aperture (i.e. the f-stop). You may need to increase the ISO get enough shutter speed. I don't know your camera at all but assuming it is a full frame or crop format SLR you could try f/11 to f/16 then ISO as high as you can get away with on your camera without getting too much image degradation and see what the gives you. You might need a tripod if there isn't a lot of light and of course you need the plants to be stationary - the slightest wind would give you motion blur...
On the other hand, having only the subject, or even part of the subject in focus is often a good thing. You make subject stand out from the image and your eyes are drawn into the in-focus subject automatically. So I wouldn't aim to have everything in focus anyway. You can experiment shooting the same image with different f-stop settings on your aperture so you can compare which ones you like the most...
I find that when I photograph flowers the images I like the most are the ones where I manage to get the subject (e.g. a single flower stem) fully into focus (or as fully as possible) and everything else to be out of focus but not too much, I still like to be able to see what the background was, just not to be in-focus. But this is just my personal preference so please don't take this as a definitive guide to shooting flowers or anything! Experiment and see what you like.
To give you a random example of where I chose too shallow DOF:
And an example which I like much more:
Not the best flower photos in the world but ones I had on my web site and they do show what I was talking about...
Best regards,
Anton