Is there any reason you need to write the data out before running it through the transformers?

You could delete the writer and reader in the red box and have it pass straight into your first transformer. You may need to use an attributerenamer to rename your fields.

Alternately you can right click on the link between your first reader and writer and click replace with attribute manager. This should contain all your field renames. Then connect the output port of the attribute manager to the input port of your first transformer

The reason behind my first data written was due to the possibility that the reader feature does not follow the standards that my organisation wanted. Hence, why I created and imported my own template as the writer feature so that the data will be in conformance with my organisation needs to suit the original data.

That is why I run it the first time so that I will get the new writer feature which matches the attributes I want and I need to set field values for the unknown fields, rearranging, removing etc... That should be the purpose of this process which why I run it twice in the same schema workbench.

I hope you can understand the flow here and I wanted to know more if I can mitigate the needs to run it twice.

Generating the desired Template Schema doesn't generally require the data to be written out like this to create features in a "Template" form.

I would probably suggest much the same as @hkingsbury​ : Replace the first Writer with an AttributeManager. In AttributeManager you can form the Schema Template desired, as it allows you to Add (Even Add NULL value fields), Remove, Reorder and Rename Attributes and even re-calculate the Attribute Values with formulae, where required.

Sending the output of the AttributeManager to a Writer will then automatically have the desired Template Schema, since AttributeManager has set the desired Schema.