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This is perfectly possible. That's how I do it on most of my sites. I will give you two options because you never told me if the daily backup and the end of month backups are supposed to be the same.

1. If they are the same. Go to Akeeba Backup, select your backup profile, scroll all the way down to the quota settings. Check “Enable remote file files quotas” and “Enable maximum backup age quotas”. Set “Maximum backup age, in days” to 31 and “Don't delete backups taken on this day of the month” to 1. Set up the upload to S3 and schedule a backup with this profile to run every day.

2. If they are different. You will need two profiles.

Daily Backups: Check “Enable remote file files quotas” and “Enable maximum backup age quotas”. Set “Maximum backup age, in days” to 31 and “Don't delete backups taken on this day of the month” to 0. Set up the upload to S3 and schedule a backup with this profile to run every day except on the 1st of each month.

Monthly backups: Do not set up quotas. Set up the upload to S3 and schedule a backup with this profile to run only on the 1st of each month.

Both backups point to the same S3 bucket and ‘directory’.

Optional (for botch use cases): you can use Amazon S3 lifecycle policies on your Amazon S3 bucket itself to transition objects (backup archives) older than 90 days to an Infrequently Accessed (IA) storage tier and backup archives older than 180 days to the S3 Glacier Deep Archive storage tier to save money on your “cold” backups. The former takes a few minutes to start downloading, the latter takes up to a few hours — but you save ~90% on storage fees on these cold backups. I've been doing that for our site's backups since we're required to keep 10 years of records and I don't fancy us paying through the nose for them — even if it's a couple hundred bucks a year.