Bike fit / correct riding position

I've been looking at buying my first road bike and am fairly settled on Decathlon's Triban 520, as that offers decent value for money. I've tried out both the medium and large frame. I'm 5'11". The frame sizes are:
M (55): 5'7" - 6'.
L (58): 5'11" - 6'1".
Both these frames felt OK to ride, and I found it difficult to choose between the two. I was testing these mainly riding on the hoods, and I didn't feel as in control (e.g. shoulder checking, signalling) as I do on my normal flat bar bikes. I also suffered from upper arm/shoulder ache after about 5 minutes - although as I was switching between the frame sizes it is difficult to attribute this to a particular size.

So, advice I'd like advice from you lovely people:

• Do people take a while to get used to the change in position, or should it feel natural straight away?
  
• Would the medium frame offer better control of the bike?
  
• I think shoulder ache may be due to how low the bars are, and I guess raising the bars could stop this. Thoughts?
  
  

For context, I usually commute around 100miles/week on flat bar bikes with out any aches or pains. Probably looking to use the Triban for longer weekend rides rather than commuting.