ok so anywhere I use my variables I have to put a '>' in front of it?
The ">" is part of the variable name, so
Set decimal [BEE Total Distance] to [BEE Total Distance] plus [{DEC:EDDI jumped distance}] (round to 0 decimal places) (save value to profile)
becomes
Set decimal [>BEE Total Distance] to [>BEE Total Distance] plus [{DEC:>EDDI jumped distance}] (round to 0 decimal places) (save value to profile)
However, as "EDDI jumped distance" is a variable set by the EDDI plugin itself(I believe), it would be
Set decimal [>BEE Total Distance] to [>BEE Total Distance] plus [{DEC:EDDI jumped distance}] (round to 0 decimal places) (save value to profile)
As stated, ">" is part of the variable name, so "EDDI jumped distance" and ">EDDI jumped distance" are not the same variable, so the plugin wouldn't set it the latter and you'd get "Not Set".
In this case it's a question of when the EDDI plugin is called to set the value. If it's before the variable is used, it'll work fine as the data you add to your internal variables is relevant to the current profile; If it's after the variable is used, the data would still pertain to the old profile.
If EDDI has to be called manually(rather than running and updating continuously in the background), you should have a command in your profile that runs on startup which calls EDDI and makes it refresh all data to make it relevant to the current profile, if you don't have that in place already.