When you say 'huge bast', do you mean a single full submission run?
There are several answers to this...
First, you need to make sure that you're deep-linking ad not hitting everything to your home page. As a matter of course, and for safety, never send more than 50% of your links to your home page. On larger sites, this should be lower.
Second, if you have other sites, then link to multiple sites in a submission run, to effectively slow it down, and help mix up the submissio profile. I.e. google doesn't end up indexing hundreds of pages all with similar titles and content and the same linked domain. So your 2nd tier properties would be perfect as an example.
Third, if you're nervous, do a percentage of them, wait a few days and then do some more. Cautious is better if you're still learning. Why would you take my or any other persons word for it. This is your business. Protect yourself and learn in stages. Don't be impatient and affect months of work with a single button click.
In all likelihood, you'd probably be ok, as long as you're not over optimised, but you need to get into the testing and measuring mind set, so that you learn from your own work and aren't reliant on others opinions.
I have an AMR testing and tips thread here:
http://www.blackhatworld.com/blackhat-seo/black-hat-seo/375944-amr-results-updated-stats-indexing.html#post3545848