So for me it sound like you are using the iBook app on your iPad and on your iPhone.
Simple solution for your described problem is, always go back to the bookshelf when you want to stop reading and your device will sync the last read position and every bookmark. On your second device i.e. the iphone you will again start iBook on the bookshelf where you left your device and voila you have the same last read location then on you iPad.
Solution = always go back to your bookshelf before stop reading for the synchronisation (you can see check the top your device for the spinning wheel which stands for intenet traffic to make sure the sync is going on).
Oh yes i don't think i have to say so but make sure you have a internet connection :-)
Your bookmarks or last read location will not synchronize i.e. if you are offline while reading and stop reading and then later go online while browsing the web for example.