Exchange 2007 is installed.
How would I use APM 3.5 to monitor if a mail store was offline?
There are some Application Templates for Exchange shipped with APM, so you can try some of them.
However I would recommend to upgrade to APM 4.0.2 SP4, because in these Service Packs for 4.0.2 (SP1 - SP4) we have updated a lot of templates (Exchange was one of them) to be more accurate and also there is PDF documentation for these templates (it provides explanation of threshold values and so)