If you have QB Online and your bank account is linked to it, there is a very easy way to record a check deposit that is made out to cover multiple invoices. Follow me:

Go to Banking tab.

Under review for that deposit: click that line where the deposit is recorded.

An additional area will drop down for that transaction and in the top left of that additional area, you will see an area where you can choose either Add, Match, or Record Transfer. Click Match. Then as long as the check amount that you deposited into your account adds up exactly to the total amount of the multiple invoices that you would like to receive payment on, QB will automatically find all of those invoices and in the deposit window, you can check and choose those invoices to receive payment on. 

Choose the correct invoices and click Save and Close. This will automatically receive payment on all the invoices you chose.

Then if you are like me and like to add additional information to each deposit (like for instance the check number and a memo stating the fact that however many invoices were paid on one check), follow me again:

Go to Sales;Invoices

Find one of the invoices you've just received payment on, and click on it to open it.

Then, in the top right of the invoice, under where it reads PAID, you'll see "1 payment made ($1234.56)" in blue writing. Click on that to view the individual deposit for that invoice. 

Here in the deposit window for that invoice you can add any detail that you would like, such as the payment method (check) or check number, and/or a memo stating which invoices were paid with 1 check, etc.

Hope this was more helpful than most. I find it very hard to find useful information on these forums and always end up playing around until I figure it out, so I thought I'd share this one and if I figure any other things out I'll continue to share in hopes of helping others. I jumped into an administrator job to help my fiance who just opened his business last year, and I really only knew the basics, so all of this is a learning curve for me, but if I can help others along the way, I'm going to because I know the feeling of needing to do something right and struggling to do so. So, again I hope this is helpful.

To All: Hope you have a great day!