Lost content when upgrading to 5s - Apps and Notes lost

I have upgraded to the 5s - I used the carphone warehouse 'geek squad' to transfer all my content but the notes and app data seem to be lost.

I had my images on an app called keep safe which seem to have dissapeared and half my notes have dissappeared (typically the important ones have gone).

I have not plugged my phone into a computer to backup for some time as I had automatic downloads to the i-cloud set up so presumed everything would save to there...am I mistaken as I cannot see a way of restoring the information.

I am worried about plugging my phone into the computer i-tunes in case it reverts back to an older version than I have at present....

If anyone can offer any tips it would be much appreciated.

Thank you in advance!!!