Moving the site to the SSL server will not introduce the complications you are assuming, in actuality, it will simplify the process to have the site on the ssl server and redirect all traffic to the ssl server.
doing it the way I recommend, you only need to configure the htaccess rule.
If you insist on only having the checkout pages under the secure server, then see the "Applying SSL to your eCart checkout" tutorial on the eCart support page:
ecart/