Hi,
In general using more than one template for model building will improve the quality of the final models. But this is true only if the different templates are complementary in the sense that some regions of one template are closer to the target structure than the corresponding regions in another template and vice versa. This will generally happen when you have several templates which are at a similar sequence identity distance from the target but are also different from each other. For example having two templates which are 40% and 45% identical to the target sequence but are only 35% identical to each other is a very good situation.
In your case you seem to have one high sequence identity template and several low sequence identity templates. It is unlikely that the low sequence identity templates will improve the model you would obtain by using only the high sequence identity template. Of course this depends on the particular case and it could be that a low sequence identity contributes something positive to the model, but it is unlikely. As a general rule it is better to build the model only on the higher sequence identity template and other templates that have similar sequence identity (given they are significantly different from each other as explained above).
With respect to the alignment of the structures: you can superpose the structures of all the templates on each other and deduce their alignment from this superposition using the MALIGN3D command in MODELLER.
I hope this helps.
Best Wishes,
Roberto