As noted in the manual and often in this forum, SAMM "assumes" standard development techniques. If the gear of the static model is not aligned, then it would appear standard techniques for the gear have not been used in the aircraft model.
This is correctable, but not without some effort on your behalf. SAMM allows you to list the model design and to adjust all parameters. You'll have to explore the static listing, (the static model is essentially the aircraft model with all animations replaced with "hardwired" transforms), find where and how the wheel orientation is used, determine the correct parameter value and set it with the parameter editor.
It might be easier to find another aircraft to convert.
Don