This document lets you keep track track of

your chemical structure numbers in a while

LaTeX document
down vote

You have two options:

1.- You can continue to use the packages {chemstyle} and
{bpchem}but yes, you should add it as
\usepackage[tracking=bpchem]{chemstyle} otherwise it won't keep
track. if you do so, you then will have to define all structures
embedded in the eps file as follows:
\begin{scheme} %this could also be figure
\schemeref[TMP1]{XjU3o9}
\CNrefnolabel{XjU3o9} %Note that this **MUST** be identical
otherwise the numbers will be different
\schemeref[TMP2]{A}
\CNrefnolabel{A}
\schemeref[TMP3]{B}
\CNrefnolabel{B}
...so on and so forth, depending on how many TMPX you have in your
scheme/figure
\includegraphics{EPSfile}
\caption{This is what appears in the bottom of the scheme/figure as
'title'}
\label{sch:Nameit!}
\end{scheme}

2.- Don't use {bpchem} as your tracking package, instead use the
newest version of {chemnum} (V 1.0). And actually if you don't want
to have schemes in your document, you don't even have to use
{chemstyle}! All you have to do is add \usepackage{chemnum} to
your preamble and then you define your labels as follows:
\begin{scheme} %in this case you MUST have the `{chemstyle}` package
loaded in your preamble
\replacecmpd{XjU3o9}
\replacecmpd{A}
\replacecmpd{B}
...so on and so forth, depending on how many TMPX you have in your
scheme/figure

 \includegraphics{EPSfile}
\caption{This is what appears in the bottom of the scheme/figure as
'title'}
\label{sch:Nameit!}
\end{scheme}

NOTE that you don't have to include TMP1 or TMPX, the program
will do it automatically, starting with TMP1, so be careful where you
place those labels in your EPS file. As far as I am concern, you can
also explicitly say which compound you want to be nicknamed A (i.e.
TMP1 or TMP4) all you have to do is add [tag=youridentifier]
between \replacecmpd and {nickname}. So for the previous example
it'll be:
\begin{scheme} %in this case you MUST have the `{chemstyle}` package
loaded in your preamble
\replacecmpd[tag=TMP3]{XjU3o9}
\replacecmpd[tag=TMP1]{A}
\replacecmpd[tag=TMP2]{B}
...so on and so forth, depending on how many TMPX you have in your
scheme/figure
\includegraphics{EPSfile}
\caption{This is what appears in the bottom of the scheme/figure as
'title'}
\label{sch:Nameit!}
\end{scheme}

And so TMP3 will be replaced by number 1, TMP1 by number 2 and

TMP2 by number 3 once you typeset your document.
I hope this is useful for someone.
This answer was also published in http://tex.stackexchange.com/
questions/51666/problems-with-numbering-compounds-usingbpchem/172526#172526 if you want further information.