Think on it well before dealing with this.
You can link one or another css on the declaration, but obviously it will work only the linked one on this view. (recommended if you don't need both)
If you link both (not recommended), the load of each can be different that you expect, creating visual glitches or loosing usabillity.
You can deal with load times expecting it to load as it's supposed (the first linked before the second one) that it's a bad idea because it depends on many things to work as it's supposed, or using javascript to make some stylesheet load after (not recommended).
Use !important statement (highly not recommended)
Why it's not recommended?
You will be overriding properties and values, making it unstable and increasing your load time, specially if you use javascript.
You'll loose the control over which property the browser is applying to an object and which not. Specially because Bootstrap will take preference over some properties even if the other css loads after (due to well accurated selectors).
!important, ironically is less important than a well accurated selector, so it only work sometimes dealing with Bootstrap. By the other part, it will make difficult each time you need to override a property value (try not to override if possible, but if needed, it's recommendable to use better selectors or different classnames or IDs to get a clean maintainable code).
What you can do?
you've different options.
The first one (the best one) is split this custom css into different css stylesheets depending on the view are needed, to avoid loading styles when there's no reference to them. The second step is to clean those css files, changing classnames to not interfere with bootstrap, and deleting possible duplicate or override of properties that bootstrap already has. You'll have a clean, fast and pretty css.
The second one is to change classnames on your css and cleaning it of possible override of properties that interfere with bootstrap.
The fastest one, if you hate a little the web owner, is simply changing classnames on your custom css, and the references to them on your HTML plus bootstrap classes:
< div class="customContainer container"> ...
And start praying for the overrides to don't cause glitches on some version of some browser.
EDIT:
You've another option, that is editing bootstrap framework classnames, which is not recommended because you'll need to produce documentation and will be less maintainable (loads of programers/designers know bootstrap but not your modified bootstrap), and you'll have to waste loads of time doing it well.