HI,
I have taken a look at your attached pdf and this looks a very interesting structure and is far from what I call a "simple" grillage. It has one curved edge and the other defined by two straights, and as the edges aren't parallel the slab parts of the composite girder are tapered.
From the pdf, I think the mesh looks well conditioned and the general layout looks good. The central section looks as though it is a solid slab over a single pier/column but I'm not sure and whether you are modelling this as a plate finite element slab or that this is also modelled as a grillage (although this is not really relevent to your questions).
From your post it seems that you have chosen to define the section properties using "design sections" from the section modules - and there is nothing wrong with this (although the prestress beam design checks will need to be done externally). You are quite right that the slab parts of the section and the precast girder parts should be kept separate, as they generally have different material properties. In this case the merge operation to combine the two elements should be used as "join" will make them one section with one material property and when assigning the properties set them as "Transformed" so the modular ration will be considered.
However, I would have preferred to use the beam module "design beams" to define each of the structural composite beams. In the beam module you cannot define tapered slabs but the beam can be made up rom a number of different sections, each with a different slab width, so you can define the same number of sections in the design beam as you have longitudinal segments in the mesh grillage and this will give a stepped representation of the tapered slab and curved edges. Using this method the correct section properties are automatically assigned to each longitudinal beam with the appropriate transformed properties. The results from the analysis can be transferred back to the beam module load tables so that the beam design and code checks can be carried out in the beam module.
I also notice that you are using the 2014 version of the software. Although this is still valid there are a number of enhancements in later versions that should be beneficial to you. For example, from 2016 versions onwards, a number of design sections and/or a number of design beams together with the structure definition can be defined in one "project" data file. The latest version is 2019, so I recommend that you upgrade to this. I also recommend that you look at example 10.1 in the examples manual which gives some general guidance. Although this is a two span parallel deck the process is the same but the beams will have multiple sections.
I hope this has been helpful to you. If this has answered your query then please mark my reply as a solution so that others can benefit from this post. Thanks
Kind regards
Dave Geeves