With some minor alterations, your code can be adapted to produce your desired output.
The couple main points you were missing to have it all:
df = pd.read_excel('container_list_master.xlsx', skiprows=range(4))
This line has the skiprows parameter which does exactly what it sounds like and allows you to skip the first few non-table lines while reading in the file.
df_output.to_excel(output_path, sheet_name=unique_value, startrow=4, index=False) Same concept for startrow as skiprows, except for writing.
- Creating a writer object, then using that writer object to put in some of your header cells as suggested in this answer, which is demonstrated below.
import pandas as pd
import os
# import openpyxl
df = pd.read_excel('container_list_master.xlsx', skiprows=range(4))
column_name = 'EAD ID'
unique_values = df[column_name].unique()
for unique_value in unique_values:
df_output = df[df[column_name].str.contains(unique_value)]
output_path = os.path.join('output', unique_value + '.xlsx')
writer = pd.ExcelWriter(output_path)
df_output.to_excel(writer, sheet_name=unique_value, startrow=4, index=False)
writer.sheets[unique_value].cell(1, 1, 'This is the template for importing ...')
writer.sheets[unique_value].cell(2, 1, 'Mapping - ArchivesSpace ... SECTION')
writer.sheets[unique_value].cell(3, 1, 'Mapping - ArchivesSpace ... FIELD')
writer.sheets[unique_value].cell(4, 1, 'ArchivesSpace field code ...')
writer.sheets[unique_value].cell(2, 2, 'Resource ...')
writer.sheets[unique_value].cell(3, 2, 'The resource ...')
writer.sheets[unique_value].cell(4, 2, 'Collection id ...')
writer.sheets[unique_value].cell(2, 3, 'Resource ...')
writer.sheets[unique_value].cell(3, 3, 'EAD ID ...')
writer.sheets[unique_value].cell(4, 3, 'ead ...')
writer.sheets[unique_value].cell(4, 4, 'res_uri')
writer.sheets[unique_value].cell(4, 5, 'ref_id')
writer.sheets[unique_value].cell(4, 6, 'title')
writer.sheets[unique_value].cell(4, 7, 'something unique')
writer.close()
Here is the input I used, which is a vague rendition of your screen cap:

And here is the output it generated:

The output looks a little tacky, but if this is just an import for a software then who cares? If the answer is you, then here is a link with information about how to format it as well: xlsx writer documentation or from another excellent answer on this site.
Let me know if you have any questions!