Is this an installation of an engine of the same type as installed before? With the same type of motor mounts? If so have you restored the engine bed mounting holes so that the new mounts can be properly and firmly installed? If not have you evaluated the engine beds and made the changes needed to accommodate the different mounts and/or engine?
Restoring the old holes is normally done by epoxying hardwood plugs in the holes.
Unless your engine installation mirrors the previous installation you should build a template for landing your new engine on your new mounts and aligning the engine with the shaft coupling. A discussion of how this is done is at http://bateau2.com/free/inboard_tpl_notes.pdf
A wealth of information on engine installation is available on the net. If you haven't already read the threads and watched the videos and visited sailors' sites that have done this and described the trials and tribulations I recommend you do that before you start. If you are a novice at this take notes and keep a record of the sites you find useful and revisit them because you won't be able to remember all the tips and advice.