Hi Paul, welcome to the forums. I'm sure someone with lots of experience will be around soon.
I got the Allez Sport 2011 a year ago as my first road bike in over 20 years, having ridden MTB in between. The MTB/hybrid bike has a more upright riding position, more shock absorbency in the tyres, and maybe a more cushioned saddle.
I found the Allez's saddle to be ok, provided I wear padded cycle shorts or a padded liner. There are plenty of guides for basic set up on the Internet, and I found having the Riva saddle pretty well level was best for me.
The saddle height: the initial setup (as stated everywhere) is to be able to put your heel on the pedal when the crank is at the bottom of the stroke (or in line with the seat tube - seems to vary by who gives the advice).
The saddle's fore/aft position: this varies for how you want to ride (or so I read). To start with, try to position the saddle so that with the cranks horizontal you can sit comfortably with your hands on top of the brake hoods, with a bend in you elbows, such that you take as little weight on your hands.
On the Allez the stem, the bit that hold the bars to the forks, has quite a bit of adjustability.
- Firstly, there are 3 spacer rings that can be used to move the stem up and down the fork's steerer tube - usually these come fitted below the stem. Note that when you lower the stem it will make the distance between the saddle and bars a little bigger - this is due to the fact that the steerer tube is angle towards the saddle.
- Next the stem has a shim inside the steerer tube clamp that can be turned around - this shim changes the stem's vertical angle between 8 and 16deg.
- Lastly the stem can be turned over so that it points more upwards, and again the shim can adjust the angle.
Oh, and you can change the handle bar angles if you prefer them to flat, or point up or down a bit.
One last thing is to use easier gears and spin the pedals faster, that way you aren't using the strength from your thighs, buttocks and hence back (they are connected) so much.
It can take a while to find the combination that works, so change one thing at a time.