Alternatively, a way that might help if the elements to be inserted can vary by each run - using XML.modify to insert the child elements into the TopLevel document.

Each child XML could easily be included or not by the use of IF statements.

-- Store the top level xml in a table (variable) so it can be used in an UPDATE statement

declare @t table(x xml);

insert @t(x) values(@toplevel);

--== Add the Employees nodes into the toplevel XML ==--

-- This requires a loop as xml.modify doesn't allow multiple updates in one batch

while exists(

-- check if there are any unprocessed elements in the empinfo xml fragment

select 1

from @t

cross apply x.nodes('//Store') tl(store)

cross apply (select tl.store.value('(StoreNumber/text())[1]','int')) as store(number)

cross apply (select @empinfo.query('(//Store[StoreNumber/text()=sql:column("store.number")]/Employees)[1]')) emp(nd)

where x.exist('(//Store[StoreNumber/text()=sql:column("store.number")]/Employees)[1]')=0

)

update top(1) t

set x.modify('insert sql:column("emp.nd") as last into (//Store[StoreNumber/text()=sql:column("store.number")])[1]')

from @t AS t

cross apply x.nodes('//Store') tl(store) -- Process each Store

cross apply (select tl.store.value('(StoreNumber/text())[1]','int')) as store(number) -- convert the StoreNumber to a non-xml data type

cross apply (select cast(@empinfo.query('(//Store[StoreNumber/text()=sql:column("store.number")]/Employees)[1]') as xml)) emp(nd) -- find the related Employees for this store

where x.exist('(//Store[StoreNumber/text()=sql:column("store.number")]/Employees)[1]')=0 -- prevent updates of existing elements

--== Add the Address nodes into the toplevel XML ==--

while exists(

select 1

from @t

cross apply x.nodes('//Store') tl(store)

cross apply (select tl.store.value('(StoreNumber/text())[1]','int')) as store(number)

cross apply (select [highlight="#ffff11"]@addinfo[/highlight].query('(//Store[StoreNumber/text()=sql:column("store.number")]/[highlight="#ffff11"]Address[/highlight])[1]')) [highlight="#ffff11"]addr[/highlight](nd)

where x.exist('(//Store[StoreNumber/text()=sql:column("store.number")]/[highlight="#ffff11"]Address[/highlight])[1]')=0

)

update top(1) t

set x.modify('insert sql:column("[highlight="#ffff11"]addr[/highlight].nd") as last into (//Store[StoreNumber/text()=sql:column("store.number")])[1]')

from @t AS t

cross apply x.nodes('//Store') tl(store)

cross apply (select tl.store.value('(StoreNumber/text())[1]','int')) as store(number)

cross apply (select cast([highlight="#ffff11"]@addinfo[/highlight].query('(//Store[StoreNumber/text()=sql:column("store.number")]/[highlight="#ffff11"]Address[/highlight])[1]') as xml)) [highlight="#ffff11"]addr[/highlight](nd)

where x.exist('(//Store[StoreNumber/text()=sql:column("store.number")]/[highlight="#ffff11"]Address[/highlight])[1]')=0

select x from @t

I have used the test data from Matt's answer, and have sections for Employees and Address.

Each new section you want to add in is then just a "copy and paste" of an existing section, then edit the highlighted parts (as seen in the Address section of my code).