The cheapest way to get to suakin is by mini-bus from Port Sudan. It is then a fair distance to walk to the old town, and when we went it was free to walk around, though I believe that has changed.
Finding a mini-bus back was more difficult. There were buses waiting, andthe assistant was shoulding 'Two more , two more'. We were 4 but he beckoned to us to come and get in. In fact there were several unfilled seats. We waited and waited until gradually a few more people arrived. We even considered paying for a couple of extra seats so that we could start moving, but in the end the bus was full and we returned to Port Sudan.
Be prepared for quite a long wait!
Suakin is easily reached from Port Sudan...I'm not exactly sure where the right bus stop in Port sudan is, but it shouldn't be too difficult to find if you ask around. The journey takes about an hour and costs 200 dinar each way.