AGM batteries ---Absorbed Glass Mat Batteries --- need a little more TLC than FLA batteries (Flooded Lead Acid batteries) & they have different charge acceptance, different internal resistance, different internal self discharge rate, & a few other things. They are different. And there are different type of AMG's (spiral, flat plate, etc.) out there as well, but more on that another day.
Also, AGM batteries are not happy if they get to hot. Max core temp for any extended period is not recommended to exceeded 125 degrees F.
In the new cars with the "stop start technology", a lot of them moved the AGM starting battery to the trunk or under the back seat, etc. - why ? - to keep it in a cooler environment than the hot under hood environment. This helps the battery last longer.
To keep the core temp under control please follow this guide line.
AGM batteries are not to be charged above 14.5 volts for any extended time period.
Also not recommended to be charged at a higher rate than 20 amp rate for any extended periods.
Also, recommend that once AGM's reach full charge, to turn the charger off or have a smart charger that reduces the charging to almost zero amps when the AGM battery is 100% full.... which is not as necessary when you have FLA batteries.
Why ? - because AGM's don't have the flooded liquid electrolyte to dissipate the core heat. As You can over heat the core of the AGM battery more easily that FLA ( Flooded Lead Acid) batteries. This can damage the battery.
(FLA) Flooded Lead Acid batteries on the other hand are very flexible in accepting how you charge them -- so as long as not in same bank, just set up the charger & charging relay for the AGM's voltages & the lead acid batteries will be OK - just charge a little slower, so a bit more time in reaching full charge.
NOTE: This would be if there is a charging relay or battery combined that combines them only when charging, but importantly not being combined when being used & especially not when they are just sitting & not wired in parallel with no disconnect between them when boat is shut down, just sitting & all is off.
I think you were using the AGM for starting & not for the house bank - so for that you should be ok as should be separate circuits.
If you have them all wired in parallel, like in a house battery bank, don't mix, as Manufactures of AGM batteries prefer for Maximum battery life to have the bank be all the same type of batteries -- either all AGM's or all Flooded.
So, Not recommended to mix them in the same bank.
One more thing to mention; I have a device called a Battery to Battery charger. It is a battery powered charger that runs off my house flooded 12-v LA batteries & I use it to charge my 24-v AGM batteries for the thruster & can be set up for AGM's & yet be powered by FLA. -- works very well & you might want to look into one of these.
Good luck with your project.