>> 
>> Is this a good idea?

Probably not.  The emacs-lisp embedded in your Org-mode file is only
re-tangled when the Org-mode file changes, so it is better to have the
conditional in the tangled Emacs Lisp file so it is run every time you
start Emacs.

>> or should I work in conditions in the emacs src blocks instead?  I
>> realize now when I'm typing it out that it might come with some other
>> issues like first time running it I would have to reinitialize emacs
>> after package installs to get my settings but after that I guess it
>> would be fine.
>
> Instead of trying to put the "look if package is present" constraint on
> Babel's side (and have a configuration file which you cannot exchange), I'd do
> it on the Emacs (Lisp) side, as I did in my configuration file [1] with a
> "try-require" function:
>
> --8<---------------cut here---------------start------------->8---
>   (defvar leuven--missing-packages nil
>     "List of packages that `try-require' or `locate-library' can't find.")
>
>   ;; require a feature/library if available; if not, fail silently
>   (defun try-require (feature)
>     "Attempt to load a library or module. Return true if the
>   library given as argument is successfully loaded. If not, instead
>   of an error, just add the package to a list of missing packages."
>     (let (time-start)
>       (condition-case err
>           ;; protected form
>           (progn
>             (when leuven-load-verbose
>               (message "(info) Checking for `%s'..." feature))
>             (if (stringp feature)
>                 (load-library feature)
>               (setq time-start (float-time))
>               (require feature))
>             t)
>         ;; error handler
>         (file-error ;; condition
>          (progn
>            (when leuven-load-verbose
>              (message "(info) Checking for `%s'... missing" feature))
>            (add-to-list 'leuven--missing-packages feature 'append))
>          nil))))
> --8<---------------cut here---------------end--------------->8---
>
> Best regards,
> Fabrice
>
> [1] https://github.com/fniessen/emacs-leuven/blob/master/emacs-leuven.el

-- 
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D