I understand that in order to execute multiple command in one line, for example save and execute pdflatex, I can do the following.
pdflatex
:w | !pdflate
Assuming <C-S-F6> actually works (it probably won't in CLI Vim), you must escape the bar or use <bar> instead:
<C-S-F6>
<bar>
:nnoremap <C-S-F6> :up \| !pdflatex %:t<CR> :nnoremap <C-S-F6> :up <bar> !pdflatex %:t<CR>
See :help map_bar.
:help map_bar