This is what has worked for me. Obviously this won't apply to all use cases but I have found that this is generally the process that I take.
Decompile the app using apktool.
apktool d appname.apk
Add the Frida gadget to the decompiled apk. You can find a gadget for your architecture here.
Put the gadget in lib/[arch]/libfrida-gadget.so
Open the AndroidManifest.xml and find the main activity path. It should look something like this:
<activity android:label="@string/app_name" android:name="com.packagename.path.to.MainActivity">
In MainActivity.smali, we need to inject libfrida-gadget.so. Ideally, we need to do it before anything else loads. We can load it using the following smali:
const-string v0, "frida-gadget"
invoke-static {v0}, Ljava/lang/System;->loadLibrary(Ljava/lang/String;)V
Which can be read as System.loadLibrary("frida-gadget"). It's important that this is done early in the app's lifecycle, so we can do it in the MainActivity static constructor. In the app that I am using, it looks like this:
.method static constructor <clinit>()V
.locals 1 # this is the number of non-param registers
...
Insert the smali above in the beginning of the static constructor (after the .locals line if present).
Now we need to rebuild the app.
apktool b -o appname_patched.apk decompiledfolder
Sign the app
jarsigner -sigalg SHA1withRSA -digestalg SHA1 -keystore my.keystore appname_patched.apk keyname
jarsigner -verify appname_patched.apk
And zipalign.
zipalign 4 appname_patched.apk appname_patched_aligned.apk
Now we can install this on our target device and use your frida library of choice to poke around. :)