If I remember correctly SRIM does not consider any crystallinity at all. The only input parameters are the layers, their thickness, the type of atoms, their stoichiometry and their density. It accounts for scattering and all its effects only in a statistical treatment, therefore any material is kind of "amorphous" for the SRIM simulation.
If you want to tell the difference of your structure, you may only be able to do so, if your density or stoichiometry is significantly different between your amorphous and crystalline phase.
For a more detailed insight, you should probably check the documentation or if you can get access to it the accompanying bock by Ziegler.
You maybe should think of X-ray diffraction or spectroscopic methods, e.g. Raman or IR, to determine crystallinity, which are probably better suited for your questions.
what Michael wrote, is OK. In crystalline materials, you can observe channeling. The scattering of ions and their energy loss is reduced for certain orientations. SRIM is very good to use for statistically disorderd materials.
SRIM suppose all the targets are amorphous. Only takes into consideration the density of the targets. To perform a damage calculation on crystalline materials, must address to MARLOWE code: https://rsicc.ornl.gov/codes/psr/psr1/psr-137.HTML or another code such as Kinetic Monte Carlos.
However, if you only want to evaluate some sopping depth and more or less, calculate the vacancies (SRIM simplifies the results, too) it is a very helpful tool.