I'm new to all of this stuff and was a bit confused. If I am timing my own splits and not using an autosplitter, my final time would be considered the time with loads, correct?

So when submitting a run do I have to myself remove the loading times and submit both times or if I just submit a time with loads will it be done by a moderator afterwards? If I have to do it myself, what would be the best way to go about doing that?

It will be considered time with loads because it's almost impossible to pause exactly when you load the game. When you submit a run that has only time with loads, i advice against trying to remove the loading times because it's very hand and not worth it and also the moderator won't be removing the loading times. If you really want to remove then use a video editing tool to do it, but again i advice against, so using the autosplitter is the best option.

So if I use an autosplitter, do I only have to submit a loadless time or will I have to submit a time with loads as well?

If you submit a run only with load times it's enough to be placed on the leaderboards, but when calculating the place for each speedrunner the time without loads is prioritized. So, in you're case if you use an autosplitter only the time without loads is mandatory, the time with loads is optional.