You will need to use OpenSSL to convert the files. On OS X, or Linux, its likely already installed. On windows you will need to download and install it.

openssl pkcs12 -export -clcerts -in server.crt -inkey server.key -out server.p12 -name "www.domain.com"

This will make a server.p12 file which contains both key files in it. You will be asked to enter a password for this, so don't forget the password or this file is useless.

Now, open Portecle. Create a new keystore of type 'JKS'. Use the 'Tools' menu, and select 'Import Key Pair...'. Import your server.p12 file. It will have you assign a password when you import this, don't forget this password as you need to set the same password when you save your keystore too. (last step)

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Now, import any other certificates this key requires, such as the root cert, intermediate cert, and cross certs. Often times these are in some form of bundle file...but you need the individual certs to import them into your keystore with Portecle.

All the files are now in your keystore, the last step is to make sure the 'chain' of those files is trusted and OK. Right click on the key pair item in the kestore, and select 'Import CA Reply...'. Choose your server.crt file used on the first step, and it should then indicate the server reply was imported successfully.

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Now you can save the keystore as something like www.domain.com.jks, and use the password from above.

Now you can reference this keystore in CrushFTP under the server preferences, Encryption, SSL tab. Or you can set it specifically on the advanced tab of a particular port.