To calculate overall accuracy assessment in eCognition using shapefiles you need to do following steps:
First, add shapefiles in to eCognition as thematic layer by modifying the project.
(make sure that points has the same projected coordinates system as your classification image)
Further two steps you can find on ecognition user guide "Creating Samples Based on a Shapefile" (img_0 in attached), but instead of 'assign class' I have used 'assign class by thematic layer' (see img_1). In my shapefiles attribute table I have three attributes OID, CIT and class names (img_2). CIT has the var. '1' for all. To extract shapefiles (in my case points) in 'condition field' i have chose [CID:Thematic Layer 1 = 1] and for thematic attribute layer 'class_name'.
Next process is "classified image objects to samples" (img_3).
So from this samples i have created TTA mask and calculate accuracy assessment via error matrix (img_4), for image object level was chosen 'classification level'.
Hope it will be helpful :)